MR DNA the best
low cost MR DNA 16s sequencing microbiome and metagenome low prices
16s rRNA Sequencing with MR DNA
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.
Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome
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).
(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.
PMID: 27171425 [PubMed - in process]
66. PLoS One. 2016 Mar 4;11(3):e0149998. doi: 10.1371/journal.pone.0149998.
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).
(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.
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
(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.
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,
(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.
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).
(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
© 2016 Asian Pacific Society of Respirology.
PMID: 26852737 [PubMed - in process]
70. Microb Biotechnol. 2014 Sep;7(5):467-79. doi: 10.1111/1751-7915.12141. Epub 2014
Determining the culturability of the rumen bacterial microbiome.
Creevey CJ(1), Kelly WJ, Henderson G, Leahy SC.
(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.
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
Stellato G(1), De Filippis F(1), La Storia A(1), Ercolini D(2).
(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.
PMID: 26341209 [PubMed - indexed for MEDLINE]
72. Bioinform Biol Insights. 2016 Apr 20;10:19-25. doi: 10.4137/BBI.S34610.
Use of Metatranscriptomics in Microbiome Research.
Bashiardes S(1), Zilberman-Schapira G(1), Elinav E(1).
(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.
PMID: 27127406 [PubMed]
73. PLoS One. 2015 Sep 11;10(9):e0137401. doi: 10.1371/journal.pone.0137401.
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).
(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.
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.
(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.
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.
(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
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).
(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 firstname.lastname@example.org
email@example.com. (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; firstname.lastname@example.org email@example.com.
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.
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
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).
(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  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,
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.
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).
(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
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
(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.
firstname.lastname@example.org. (8)Biotechnology Institute, University of Minnesota, St. Paul,
MN, 55108, USA. email@example.com.
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.
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,
(1)1Department of Microbiology, Immunology, and Tropical Medicine, School of
Medicine and Health Sciences, George Washington University, Washington D.C., USA.
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.
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).
(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.
PMID: 24454771 [PubMed - indexed for MEDLINE]
16s rRNA Sequencing with MR DNA
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.
16s sequencing illumina or PGM low cost prices with MR DNA