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16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.


1921.65. 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]



66. PLoS One. 2016 Mar 4;11(3):e0149998. doi: 10.1371/journal.pone.0149998.

eCollection 2016.


Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum

Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease.


Hogan DA(1), Willger SD(1), Dolben EL(1), Hampton TH(1), Stanton BA(1), Morrison

HG(2), Sogin ML(2), Czum J(3), Ashare A(4).


Author information:

(1)Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover,

NH, United States of America. (2)Josephine Bay Paul Center for Comparative

Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA,

United States of America. (3)Department of Radiology, Dartmouth-Hitchcock Medical

Center, Lebanon, NH, United States of America. (4)Pulmonary and Critical Care

Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of



Individuals with cystic fibrosis (CF) often acquire chronic lung infections that

lead to irreversible damage. We sought to examine regional variation in the

microbial communities in the lungs of individuals with mild-to-moderate CF lung

disease, to examine the relationship between the local microbiota and local

damage, and to determine the relationships between microbiota in samples taken

directly from the lung and the microbiota in spontaneously expectorated sputum.

In this initial study, nine stable, adult CF patients with an FEV1>50% underwent

regional sampling of different lobes of the right lung by bronchoalveolar lavage

(BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were

obtained from six of the nine subjects immediately prior to the procedure.

Microbial community analysis was performed on DNA extracted from these samples

and the extent of damage in each lobe was quantified from a recent CT scan. The

extent of damage observed in regions of the right lung did not correlate with

specific microbial genera, levels of community diversity or composition, or

bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from

different regions of the lung contained similar microbial communities. In eight

out of nine subjects, PB samples from different regions of the lung were also

similar in microbial community composition, and were similar to microbial

communities in BAL fluid from the same lobe. Microbial communities in PB samples

were more diverse than those in BAL samples, suggesting enrichment of some taxa

in mucus plugs. To our knowledge, this study is the first to examine the

microbiota in different regions of the CF lung in clinically stable individuals

with mild-to-moderate CF-related lung disease.


DOI: 10.1371/journal.pone.0149998

PMCID: PMC4778801

PMID: 26943329  [PubMed - indexed for MEDLINE]



67. J Asthma. 2015;52(9):873-80. doi: 10.3109/02770903.2015.1028076. Epub 2015 Oct



Home dust microbiota is disordered in homes of low-income asthmatic children.


Ciaccio CE(1), Barnes C(1), Kennedy K(1), Chan M(1), Portnoy J(1), Rosenwasser



Author information:

(1)a Department of Pediatrics and the Center for Environmental Health ,

Children's Mercy Hospital , Kansas City , MO , USA.


OBJECTIVE: Exposure to microorganisms has repeatedly been found to influence

development of atopic diseases, such as asthma. Innovative techniques have been

developed that can comprehensively characterize microbial communities. The

objective of this study was to characterize the home microbiota of asthmatic

children utilizing 16S rRNA-based phylogenetic analysis by microarray.

METHODS: In this cross-sectional study, DNA was extracted from home dust and

bacterial 16S rRNA genes amplified. Bacterial products were hybridized to the

PhyloChip Array and scanned using a GeneArray scanner (Affymetrix, Santa Clara,

CA). The Adonis test was used to determine significant differences in the whole

microbiome. Welch's t-test was used to determine significant abundance

differences and genus-level richness differences.

RESULTS: Nineteen homes were included in the analysis (14 asthma and five no

asthma). About 1741 operational taxonomic units (OTUs) were found in at least one

sample. Bacterial genus richness did not differ in the homes of asthmatics and

non-asthmatics (p = 0.09). The microbial profile was significantly different

between the two groups (p = 0.025). All the top 12 OTUs with significant

abundance differences were increased in homes of asthmatics and belonged to one

of the five phyla (p = 0.001 to p = 7.2 × 10(-6)). Nearly half of significant

abundance differences belonged to the phylum Cyanobacteria or Proteobacteria.

CONCLUSIONS: These results suggest that home dust has a characteristic microbiota

which is disturbed in the homes of asthmatics, resulting in a particular

abundance of Cyanobacteria and Proteobacteria. Further investigations are needed

which utilize high-throughput technology to further clarify how home microbial

exposures influence human health and disease.


DOI: 10.3109/02770903.2015.1028076

PMCID: PMC4807694 [Available on 2016-11-01]

PMID: 26512904  [PubMed - indexed for MEDLINE]



68. Mol Ecol. 2014 Sep;23(18):4498-510. doi: 10.1111/mec.12885. Epub 2014 Sep 8.


The Sphagnum microbiome supports bog ecosystem functioning under extreme



Bragina A(1), Oberauner-Wappis L, Zachow C, Halwachs B, Thallinger GG, Müller H,

Berg G.


Author information:

(1)Institute of Environmental Biotechnology, Graz University of Technology,

Petersgasse 12, 8010, Graz, Austria.


Sphagnum-dominated bogs represent a unique yet widely distributed type of

terrestrial ecosystem and strongly contribute to global biosphere functioning.

Sphagnum is colonized by highly diverse microbial communities, but less is known

about their function. We identified a high functional diversity within the

Sphagnum microbiome applying an Illumina-based metagenomic approach followed by

de novo assembly and MG-RAST annotation. An interenvironmental comparison

revealed that the Sphagnum microbiome harbours specific genetic features that

distinguish it significantly from microbiomes of higher plants and peat soils.

The differential traits especially support ecosystem functioning by a symbiotic

lifestyle under poikilohydric and ombrotrophic conditions. To realise a

plasticity-stability balance, we found abundant subsystems responsible to cope

with oxidative and drought stresses, to exchange (mobile) genetic elements, and

genes that encode for resistance to detrimental environmental factors, repair and

self-controlling mechanisms. Multiple microbe-microbe and plant-microbe

interactions were also found to play a crucial role as indicated by diverse genes

necessary for biofilm formation, interaction via quorum sensing and nutrient

exchange. A high proportion of genes involved in nitrogen cycle and recycling of

organic material supported the role of bacteria for nutrient supply. 16S rDNA

analysis indicated a higher structural diversity than that which had been

previously detected using PCR-dependent techniques. Altogether, the diverse

Sphagnum microbiome has the ability to support the life of the host plant and the

entire ecosystem under changing environmental conditions. Beyond this, the moss

microbiome presents a promising bio-resource for environmental biotechnology -

with respect to novel enzymes or stress-protecting bacteria.


© 2014 John Wiley & Sons Ltd.


DOI: 10.1111/mec.12885

PMID: 25113243  [PubMed - indexed for MEDLINE]



69. Respirology. 2016 May;21(4):590-9. doi: 10.1111/resp.12732. Epub 2016 Jan 27.


COPD and the microbiome.


Mammen MJ(1,)(2), Sethi S(1,)(3).


Author information:

(1)Divisions of Pulmonary, Critical Care, and Sleep Medicine, State University of

New York at Buffalo School of Medicine, Buffalo, New York, USA. (2)Department of

Biomedical Informatics, State University of New York at Buffalo School of

Medicine, Buffalo, New York, USA. (3)Veterans Affairs Western New York Healthcare

System, Buffalo, New York, USA.


Traditional culture techniques confirm that bacteria have an important role in

Chronic Obstructive Pulmonary Disease (COPD). In individuals with COPD,

acquisition of novel bacterial strains is associated with onset of acute

exacerbation of COPD, which leads to further lung dysfunction and enormous

health-care costs. Recent study of the human microbiome, the total composite of

the bacteria on the human body, posited the microbiome as the last human organ

studied, as the microbiome performs a multitude of metabolic functions absent in

the human genome. The largest project to study the human microbiome was the

National Institutes of Health (NIH) human microbiome project (HMP) started in

2007 to understand the 'normal' microbiome. However due to the presumption that

the healthy human lung was sterile, the respiratory tract was not included in

that study. The advent of next-generation sequencing technologies has allowed the

investigation of the human respiratory microbiome, which revealed that the

healthy lung does have a robust microbiome. Subsequent studies in individuals

with COPD revealed that the microbiome composition fluctuates with severity of

COPD, composition of the individual aero-digestive tract microbiomes, age, during

an acute exacerbation of COPD and with the use of steroids and/or antibiotics.

Understanding the impact of the microbiome on COPD progression and risk of

exacerbation will lead to directed therapies for prevention of COPD progression

and exacerbation.


© 2016 Asian Pacific Society of Respirology.


DOI: 10.1111/resp.12732

PMID: 26852737  [PubMed - in process]



70. Microb Biotechnol. 2014 Sep;7(5):467-79. doi: 10.1111/1751-7915.12141. Epub 2014

Jul 1.


Determining the culturability of the rumen bacterial microbiome.


Creevey CJ(1), Kelly WJ, Henderson G, Leahy SC.


Author information:

(1)Animal and Bioscience Research Department, Animal and Grassland Research and

Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland; Institute of

Biological, Environmental and Rural Sciences, Aberystwyth University,

Aberystwyth, Ceredigion, UK.


The goal of the Hungate1000 project is to generate a reference set of rumen

microbial genome sequences. Toward this goal we have carried out a meta-analysis

using information from culture collections, scientific literature, and the NCBI

and RDP databases and linked this with a comparative study of several rumen 16S

rRNA gene-based surveys. In this way we have attempted to capture a snapshot of

rumen bacterial diversity to examine the culturable fraction of the rumen

bacterial microbiome. Our analyses have revealed that for cultured rumen

bacteria, there are many genera without a reference genome sequence. Our

examination of culture-independent studies highlights that there are few novel

but many uncultured taxa within the rumen bacterial microbiome. Taken together

these results have allowed us to compile a list of cultured rumen isolates that

are representative of abundant, novel and core bacterial species in the rumen. In

addition, we have identified taxa, particularly within the phylum Bacteroidetes,

where further cultivation efforts are clearly required. This information is being

used to guide the isolation efforts and selection of bacteria from the rumen

microbiota for sequencing through the Hungate1000.


© 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd

and Society for Applied Microbiology.


DOI: 10.1111/1751-7915.12141

PMCID: PMC4229327

PMID: 24986151  [PubMed - indexed for MEDLINE]



71. Appl Environ Microbiol. 2015 Nov;81(22):7893-904. doi: 10.1128/AEM.02294-15. Epub

2015 Sep 4.


Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy

Processing Environment.


Stellato G(1), De Filippis F(1), La Storia A(1), Ercolini D(2).


Author information:

(1)Department of Agricultural Sciences, Division of Microbiology, University of

Naples Federico II, Portici, Italy. (2)Department of Agricultural Sciences,

Division of Microbiology, University of Naples Federico II, Portici, Italy



Microbial contamination in food processing plants can play a fundamental role in

food quality and safety. In this study, the microbiota in a dairy plant was

studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput

amplicon sequencing. Environmental samples from surfaces and tools were studied

along with the different types of cheese produced in the same plant. The

microbiota of environmental swabs was very complex, including more than 200

operational taxonomic units with extremely variable relative abundances (0.01 to

99%) depending on the species and sample. A core microbiota shared by 70% of the

samples indicated a coexistence of lactic acid bacteria with a remarkable level

of Streptococcus thermophilus and possible spoilage-associated bacteria,

including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative

abundance above 50%. The most abundant yeasts were Kluyveromyces marxianus,

Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii.

Beta-diversity analyses showed a clear separation of environmental and cheese

samples based on both yeast and bacterial community structure. In addition,

predicted metagenomes also indicated differential distribution of metabolic

pathways between the two categories of samples. Cooccurrence and coexclusion

pattern analyses indicated that the occurrence of potential spoilers was excluded

by lactic acid bacteria. In addition, their persistence in the environment can be

helpful to counter the development of potential spoilers that may contaminate the

cheeses, with possible negative effects on their microbiological quality.


Copyright © 2015, American Society for Microbiology. All Rights Reserved.


DOI: 10.1128/AEM.02294-15

PMCID: PMC4616952

PMID: 26341209  [PubMed - indexed for MEDLINE]



72. Bioinform Biol Insights. 2016 Apr 20;10:19-25. doi: 10.4137/BBI.S34610.

eCollection 2016.


Use of Metatranscriptomics in Microbiome Research.


Bashiardes S(1), Zilberman-Schapira G(1), Elinav E(1).


Author information:

(1)Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.


The human intestinal microbiome is a microbial ecosystem that expresses as many

as 100 times more genes than the human host, thereby constituting an important

component of the human holobiome, which contributes to multiple health and

disease processes. As most commensal species are difficult or impossible to

culture, genomic characterization of microbiome composition and function, under

various environmental conditions, comprises a central tool in understanding its

roles in health and disease. The first decade of microbiome research was mainly

characterized by usage of DNA sequencing-based 16S rDNA and shotgun metagenome

sequencing, allowing for the elucidation of microbial composition and genome

structure. Technological advances in RNA-seq have recently provided us with an

ability to gain insight into the genes that are actively expressed in complex

bacterial communities, enabling the elucidation of the functional changes that

dictate the microbiome functions at given contexts, its interactions with the

host, and functional alterations that accompany the conversion of a healthy

microbiome toward a disease-driving configuration. Here, we highlight some of the

key metatranscriptomics strategies that are implemented to determine microbiota

gene expression and its regulation and discuss the advantages and potential

challenges associated with these approaches.


DOI: 10.4137/BBI.S34610

PMCID: PMC4839964

PMID: 27127406  [PubMed]



73. PLoS One. 2015 Sep 11;10(9):e0137401. doi: 10.1371/journal.pone.0137401.

eCollection 2015.


Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using

Deep 16sRNA Pyrosequencing.


Kreisinger J(1), Čížková D(2), Kropáčková L(3), Albrecht T(4).


Author information:

(1)Studenec Research Facility, Institute of Vertebrate Biology, Academy of

Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic; Department

of Zoology, Faculty of Science, Charles University Prague, Viničná 7, 128 44

Prague 2, Czech Republic; Department of Biodiversity and Molecular Ecology,

Fondazione Edmund Mach, Research and Innovation Centre, I-38010 San Michele

all'Adige, TN, Italy. (2)Studenec Research Facility, Institute of Vertebrate

Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech

Republic. (3)Department of Zoology, Faculty of Science, Charles University

Prague, Viničná 7, 128 44 Prague 2, Czech Republic. (4)Studenec Research

Facility, Institute of Vertebrate Biology, Academy of Sciences of the Czech

Republic, Květná 8, 603 65 Brno, Czech Republic; Department of Zoology, Faculty

of Science, Charles University Prague, Viničná 7, 128 44 Prague 2, Czech



Effects of vertebrate-associated microbiota on physiology and health are of

significant interest in current biological research. Most previous studies have

focused on host-microbiota interactions in captive-bred mammalian models. These

interactions and their outcomes are still relatively understudied, however, in

wild populations and non-mammalian taxa. Using deep pyrosequencing, we described

the cloacal microbiome (CM) composition in free living barn swallows Hirundo

rustica, a long-distance migratory passerine bird. Barn swallow CM was dominated

by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla.

Bacteroidetes, which represent an important proportion of the digestive tract

microbiome in many vertebrate species, was relatively rare in barn swallow CM (<

5%). CM composition did not differ between males and females. A significant

correlation of CM within breeding pair members is consistent with the hypothesis

that cloacal contact during within-pair copulation may promote transfer of

bacterial assemblages. This effect on CM composition had a relatively low effect

size, however, possibly due to the species' high level of sexual promiscuity.


DOI: 10.1371/journal.pone.0137401

PMCID: PMC4567286

PMID: 26360776  [PubMed - indexed for MEDLINE]



74. Diabetes. 2013 Oct;62(10):3341-9. doi: 10.2337/db13-0844.


Assessing the human gut microbiota in metabolic diseases.


Karlsson F(1), Tremaroli V, Nielsen J, Bäckhed F.


Author information:

(1)Department of Chemical and Biological Engineering, Chalmers University of

Technology, Gothenburg, Sweden.


Recent findings have demonstrated that the gut microbiome complements our human

genome with at least 100-fold more genes. In contrast to our Homo sapiens-derived

genes, the microbiome is much more plastic, and its composition changes with age

and diet, among other factors. An altered gut microbiota has been associated with

several diseases, including obesity and diabetes, but the mechanisms involved

remain elusive. Here we discuss factors that affect the gut microbiome, how the

gut microbiome may contribute to metabolic diseases, and how to study the gut

microbiome. Next-generation sequencing and development of software packages have

led to the development of large-scale sequencing efforts to catalog the human

microbiome. Furthermore, the use of genetically engineered gnotobiotic mouse

models may increase our understanding of mechanisms by which the gut microbiome

modulates host metabolism. A combination of classical microbiology, sequencing,

and animal experiments may provide further insights into how the gut microbiota

affect host metabolism and physiology.


DOI: 10.2337/db13-0844

PMCID: PMC3781439

PMID: 24065795  [PubMed - indexed for MEDLINE]



75. Inflamm Bowel Dis. 2015 Nov;21(11):2515-32. doi: 10.1097/MIB.0000000000000549.


Metagenomic Analysis of Crohn's Disease Patients Identifies Changes in the Virome

and Microbiome Related to Disease Status and Therapy, and Detects Potential

Interactions and Biomarkers.


Pérez-Brocal V(1), García-López R, Nos P, Beltrán B, Moret I, Moya A.


Author information:

(1)*Genomics and Health Area, Fundación para el Fomento de la Investigación

Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública,

Valencia, Spain; †Institut Cavanilles de Biodiversitat i Biologia Evolutiva,

Universitat de València, Paterna, Spain; ‡CIBER en Epidemiología y Salud Pública

(CIBERESP), Madrid, Spain; §Servicio de Medicina Digestiva, Hospital Universitari

i Politècnic La Fe, Valencia, Spain; ‖CIBER en Enfermedades Hepáticas y

Digestivas (CIBEREHD), Madrid, Spain; and ¶Servicio de Medicina Digestiva,

Instituto de Investigación Sanitaria La Fe, Valencia, Spain.


BACKGROUND: The aim of this study was to survey the bacterial and viral

communities in different types of samples from patients with Crohn's disease (CD)

at different stages of the disease to relate their distribution with the origin

and progression of this disorder.

METHODS: A total of 42 fecal samples and 15 biopsies from 20 patients with CD and

20 healthy control individuals were collected for bacterial 16S rRNA gene

profiling and DNA/RNA virome metagenomic analysis through 454 pyrosequencing.

Their composition, abundance, and diversity were analyzed, and comparisons of

disease status, patient status, and sample origin were used to determine

statistical differences between the groups.

RESULTS: Bacterial composition and relative abundance in new-onset patients with

CD differed markedly from control individuals. Individual variability and sample

origin had a stronger impact on viral communities than the disease, contrary to

what was observed for bacterial populations although increased numbers of

overrepresented viruses were observed in feces from patients with CD.

Correlation-based networks were constructed to show potential relations between

bacteria and between those and viruses.

CONCLUSIONS: The bacterial community reflects the disease status of individuals

more accurately than their viral counterparts. However, numerous viral biomarkers

specifically associated with CD disease were identified. Because viruses can

modulate bacterial communities, the correlation networks between both communities

constitute a step forward in unraveling their interactions under normal and CD

disease conditions.


DOI: 10.1097/MIB.0000000000000549

PMID: 26313691  [PubMed - indexed for MEDLINE]



76. Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):E2875-84. doi:

10.1073/pnas.1409644111. Epub 2014 Jun 25.


Oligotyping analysis of the human oral microbiome.


Eren AM(1), Borisy GG(2), Huse SM(3), Mark Welch JL(4).


Author information:

(1)Josephine Bay Paul Center for Comparative Molecular Biology and Evolution,

Marine Biological Laboratory, Woods Hole, MA 02543; (2)Department of

Microbiology, The Forsyth Institute, Cambridge, MA 02142; and gborisy@forsyth.org

jmarkwelch@mbl.edu. (3)Department of Pathology and Laboratory Medicine, Brown

University, Providence, RI 02912. (4)Josephine Bay Paul Center for Comparative

Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA

02543; gborisy@forsyth.org jmarkwelch@mbl.edu.


The Human Microbiome Project provided a census of bacterial populations in

healthy individuals, but an understanding of the biomedical significance of this

census has been hindered by limited taxonomic resolution. A high-resolution

method termed oligotyping overcomes this limitation by evaluating individual

nucleotide positions using Shannon entropy to identify the most information-rich

nucleotide positions, which then define oligotypes. We have applied this method

to comprehensively analyze the oral microbiome. Using Human Microbiome Project

16S rRNA gene sequence data for the nine sites in the oral cavity, we identified

493 oligotypes from the V1-V3 data and 360 oligotypes from the V3-V5 data. We

associated these oligotypes with species-level taxon names by comparison with the

Human Oral Microbiome Database. We discovered closely related oligotypes,

differing sometimes by as little as a single nucleotide, that showed dramatically

different distributions among oral sites and among individuals. We also detected

potentially pathogenic taxa in high abundance in individual samples. Numerous

oligotypes were preferentially located in plaque, others in keratinized gingiva

or buccal mucosa, and some oligotypes were characteristic of habitat groupings

such as throat, tonsils, tongue dorsum, hard palate, and saliva. The differing

habitat distributions of closely related oligotypes suggest a level of ecological

and functional biodiversity not previously recognized. We conclude that the

Shannon entropy approach of oligotyping has the capacity to analyze entire

microbiomes, discriminate between closely related but distinct taxa and, in

combination with habitat analysis, provide deep insight into the microbial

communities in health and disease.


DOI: 10.1073/pnas.1409644111

PMCID: PMC4104879

PMID: 24965363  [PubMed - indexed for MEDLINE]



77. Sci Rep. 2014 Nov 11;4:6990. doi: 10.1038/srep06990.


Distinct composition of the oral indigenous microbiota in South Korean and

Japanese adults.


Takeshita T(1), Matsuo K(2), Furuta M(1), Shibata Y(1), Fukami K(1), Shimazaki

Y(3), Akifusa S(4), Han DH(5), Kim HD(5), Yokoyama T(6), Ninomiya T(7), Kiyohara

Y(7), Yamashita Y(1).


Author information:

(1)Section of Preventive and Public Health Dentistry, Division of Oral Health,

Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka,

Japan. (2)1] Section of Preventive and Public Health Dentistry, Division of Oral

Health, Growth and Development, Kyushu University Faculty of Dental Science,

Fukuoka, Japan [2] Section of Dental Anesthesiology, Division of Maxillofacial

Diagnostic and Surgical Sciences, Kyushu University Faculty of Dental Science,

Fukuoka, Japan. (3)Department of Preventive Dentistry and Dental Public Health,

School of Dentistry, Aichi-Gakuin University, Nagoya, Japan. (4)Department of

Oral Health Management, School of Oral Health Science, Kyushu Dental University,

Kitakyushu, Japan. (5)Department of Preventive and Social Dentistry, School of

Dentistry, Seoul National University, Seoul, Korea. (6)Section of Dental

Anesthesiology, Division of Maxillofacial Diagnostic and Surgical Sciences,

Kyushu University Faculty of Dental Science, Fukuoka, Japan. (7)Department of

Environmental Medicine, Graduate School of Medical Sciences, Kyushu University,

Fukuoka, Japan.


A comparison of national surveys on oral health suggested that the population of

South Korea has a better periodontal health status than that of Japan, despite

their similar inherent backgrounds. Here, we investigated differences in oral

bacterial assemblages between individuals from those two countries. To exclude

potential effects of oral health condition on the microbiota, we selected 52

Korean and 88 Japanese orally healthy adults (aged 40-79 years) from the

participants of two cohort studies, the Yangpyeong study in South Korea and the

Hisayama study in Japan, and compared the salivary microbiomes. The microbiota of

the Japanese individuals comprised a more diverse community, with greater

proportions of 17 bacterial genera, including Veillonella, Prevotella, and

Fusobacterium, compared to the microbiota of the Korean individuals. Conversely,

Neisseria and Haemophilus species were present in much lower proportions in the

microbiota of the Japanese individuals than the Korean individuals. Because

higher proportions of Prevotella and Veillonella and lower proportions of

Neisseria and Haemophilus in the salivary microbiome were implicated in

periodontitis, the results of this study suggest that the greater proportion of

dysbiotic oral microbiota in the Japanese individuals is associated with their

higher susceptibility to periodontitis compared to the Korean individuals.


DOI: 10.1038/srep06990

PMCID: PMC4227031

PMID: 25384884  [PubMed - indexed for MEDLINE]



78. BMC Genomics. 2014 Dec 12;15:1096. doi: 10.1186/1471-2164-15-1096.


Functional genomics and microbiome profiling of the Asian longhorned beetle

(Anoplophora glabripennis) reveal insights into the digestive physiology and

nutritional ecology of wood feeding beetles.


Scully ED, Geib SM, Carlson JE, Tien M, McKenna D, Hoover K(1).


Author information:

(1)Department of Entomology and Center for Chemical Ecology, The Pennsylvania

State University, 501 ASI Building, University Park, PA 16802, USA.



BACKGROUND: Wood-feeding beetles harbor an ecologically rich and taxonomically

diverse assemblage of gut microbes that appear to promote survival in woody

tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the

contributions of these apparent symbionts to digestive physiology and nutritional

ecology remain uncharacterized in most beetle lineages.

RESULTS: Through parallel transcriptome profiling of beetle- and microbial-

derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned

beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is

enriched in biosynthetic pathways for the synthesis of essential amino acids,

vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can

provide essential nutrients that the beetle cannot obtain from its woody diet or

synthesize itself. The beetle gut microbiota also produce their own suite of

transcripts that can enhance lignin degradation, degrade hemicellulose, and

ferment xylose and wood sugars. An abundance of cellulases from several glycoside

hydrolase families are expressed endogenously by A. glabripennis, as well as

transcripts that allow the beetle to convert microbe-synthesized essential amino

acids into non-essential amino acids. A. glabripennis and its gut microbes likely

collaborate to digest carbohydrates and convert released sugars and amino acid

intermediates into essential nutrients otherwise lacking from their woody host


CONCLUSIONS: The nutritional provisioning capabilities of the A. glabripennis gut

microbiome may contribute to the beetles' unusually broad host range. The

presence of some of the same microbes in the guts of other Cerambycidae and other

wood-feeding beetles suggests that partnerships with microbes may be a

facilitator of evolutionary radiations in beetles, as in certain other groups of

insects, allowing access to novel food sources through enhanced nutritional



DOI: 10.1186/1471-2164-15-1096

PMCID: PMC4299006

PMID: 25495900  [PubMed - indexed for MEDLINE]



79. Genome Med. 2016 Apr 28;8(1):49. doi: 10.1186/s13073-016-0301-4.


Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection.


Montassier E(1,)(2), Al-Ghalith GA(2,)(3), Ward T(4), Corvec S(1,)(5), Gastinne

T(6), Potel G(1), Moreau P(6), de la Cochetiere MF(1), Batard E(1), Knights



Author information:

(1)Université de Nantes, EA 3826 Thérapeutiques cliniques et expérimentales des

infections. Faculté de médecine, 1 Rue G Veil, Nantes, 44000, France.

(2)Department of Computer Science and Engineering, University of Minnesota,

Minneapolis, MN, 55455, USA. (3)Biomedical Informatics and Computational Biology,

University of Minnesota, Minneapolis, MN, 55455, USA. (4)Biotechnology Institute,

University of Minnesota, St. Paul, MN, 55108, USA. (5)Nantes University Hospital,

Microbiology Laboratory, Nantes, France. (6)Hematology Department, Nantes

University Hospital, Nantes, France. (7)Department of Computer Science and

Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.

dknights@umn.edu. (8)Biotechnology Institute, University of Minnesota, St. Paul,

MN, 55108, USA. dknights@umn.edu.


Erratum in

    Genome Med. 2016;8(1):61.


BACKGROUND: Bacteremia, or bloodstream infection (BSI), is a leading cause of

death among patients with certain types of cancer. A previous study reported that

intestinal domination, defined as occupation of at least 30 % of the microbiota

by a single bacterial taxon, is associated with BSI in patients undergoing

allo-HSCT. However, the impact of the intestinal microbiome before treatment

initiation on the risk of subsequent BSI remains unclear. Our objective was to

characterize the fecal microbiome collected before treatment to identify microbes

that predict the risk of BSI.

METHODS: We sampled 28 patients with non-Hodgkin lymphoma undergoing allogeneic

hematopoietic stem cell transplantation (HSCT) prior to administration of

chemotherapy and characterized 16S ribosomal RNA genes using high-throughput DNA

sequencing. We quantified bacterial taxa and used techniques from machine

learning to identify microbial biomarkers that predicted subsequent BSI.

RESULTS: We found that patients who developed subsequent BSI exhibited decreased

overall diversity and decreased abundance of taxa including Barnesiellaceae,

Coriobacteriaceae, Faecalibacterium, Christensenella, Dehalobacterium,

Desulfovibrio, and Sutterella. Using machine-learning methods, we developed a BSI

risk index capable of predicting BSI incidence with a sensitivity of 90 % at a

specificity of 90 % based only on the pretreatment fecal microbiome.

CONCLUSIONS: These results suggest that the gut microbiota can identify high-risk

patients before HSCT and that manipulation of the gut microbiota for prevention

of BSI in high-risk patients may be a useful direction for future research. This

approach may inspire the development of similar microbiome-based diagnostic and

prognostic models in other diseases.


DOI: 10.1186/s13073-016-0301-4

PMCID: PMC4848771

PMID: 27121964  [PubMed - in process]



80. FASEB J. 2013 Nov;27(11):4572-84. doi: 10.1096/fj.13-232751. Epub 2013 Aug 7.


Infection with the carcinogenic liver fluke Opisthorchis viverrini modifies

intestinal and biliary microbiome.


Plieskatt JL(1), Deenonpoe R, Mulvenna JP, Krause L, Sripa B, Bethony JM,

Brindley PJ.


Author information:

(1)1Department of Microbiology, Immunology, and Tropical Medicine, School of

Medicine and Health Sciences, George Washington University, Washington D.C., USA.

P.J.B., pbrindley@gwu.edu.


Opisthorchis viverrini is a fish-borne trematode endemic in East Asia. Following

ingestion, the flukes locate to the biliary tre where chronic infection

frequently leads to cholangiocarcinoma (CCA). The mechanisms by which O.

viverrini infection culminates in CCA remain unknown. An unexplored aspect is its

influence on the host microbiome. In the hamster, infection with this pathogen

reliably leads to CCA. Genomic DNAs of microbiota from colorectal contents and

bile of hamsters and from whole O. viverrini were examined in this model of

fluke-induced CCA. Microbial communities were characterized by high-throughput

sequencing of variable regions 7-9 of prokaryotic 16S ribosomal DNA. Of ∼1

million sequences, 536,009 with useable reads were assignable to 29,776

operational taxonomy units (OTUs) and, in turn, to 20 phyla and 273 genera of

Bacteria or Archaea. Microbial community analyses revealed that fluke infection

perturbed the gastrointestinal tract microbiome, increasing Lachnospiraceae,

Ruminococcaceae, and Lactobacillaceae, while decreasing Porphyromonadaceae,

Erysipelotrichaceae, and Eubacteriaceae (P≤0.05). More than 60 OTUs were detected

in the biliary system, which confirmed bacteriobilia and a noteworthy community

of microbes associated with the parasites. The fluke-associated microorganisms

included potential pathogens from the Enterobacteriaceae and Listeriaceae and

others, including Cyanobacteria and Deinococci, usually found in external

environments. Given that opisthorchiasis is distinguished from other helminth

infections by a robust inflammatory phenotype with conspicuously elevated IL-6,

and that inflammation of the biliary system leads to periductal fibrosis, which

is a precursor of CCA, the flukes and their microbiota may together drive this

distinctive immune response.


DOI: 10.1096/fj.13-232751

PMCID: PMC3804743

PMID: 23925654  [PubMed - indexed for MEDLINE]




109. PLoS One. 2014 Jan 15;9(1):e84963. doi: 10.1371/journal.pone.0084963. eCollection



Recruiting human microbiome shotgun data to site-specific reference genomes.


Xie G(1), Lo CC(1), Scholz M(1), Chain PS(1).


Author information:

(1)Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico,

United States of America ; Microbial and Metagenome Program, Joint Genome

Institute, Walnut Creek, California, United States of America.


The human body consists of innumerable multifaceted environments that predispose

colonization by a number of distinct microbial communities, which play

fundamental roles in human health and disease. In addition to community surveys

and shotgun metagenomes that seek to explore the composition and diversity of

these microbiomes, there are significant efforts to sequence reference microbial

genomes from many body sites of healthy adults. To illustrate the utility of

reference genomes when studying more complex metagenomes, we present a

reference-based analysis of sequence reads generated from 55 shotgun metagenomes,

selected from 5 major body sites, including 16 sub-sites. Interestingly, between

13% and 92% (62.3% average) of these shotgun reads were aligned to a

then-complete list of 2780 reference genomes, including 1583 references for the

human microbiome. However, no reference genome was universally found in all body

sites. For any given metagenome, the body site-specific reference genomes,

derived from the same body site as the sample, accounted for an average of 58.8%

of the mapped reads. While different body sites did differ in abundant genera,

proximal or symmetrical body sites were found to be most similar to one another.

The extent of variation observed, both between individuals sampled within the

same microenvironment, or at the same site within the same individual over time,

calls into question comparative studies across individuals even if sampled at the

same body site. This study illustrates the high utility of reference genomes and

the need for further site-specific reference microbial genome sequencing, even

within the already well-sampled human microbiome.


DOI: 10.1371/journal.pone.0084963

PMCID: PMC3893169

PMID: 24454771  [PubMed - indexed for MEDLINE]






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