16s microbiome and metagenomes Can you see the Microbes?
Uncover the World of Microbiomes!! 3K to 20K Reads for as low as $60











MR DNA for microbiome and 16s sequencing


148. Genome Med. 2014 Nov 15;6(11):99. doi: 10.1186/s13073-014-0099-x. eCollection



The conjunctival microbiome in health and trachomatous disease: a case control



Zhou Y(1), Holland MJ(2), Makalo P(3), Joof H(3), Roberts CH(2), Mabey DC(2),

Bailey RL(2), Burton MJ(2), Weinstock GM(4), Burr SE(5).


Author information:

(1)The Genome Institute, Washington University, St Louis, MO 63108 USA ;

Department of Pediatrics, Washington University School of Medicine, St Louis, MO

63130 USA. (2)Department of Clinical Research, London School of Hygiene and

Tropical Medicine, London, WC1E 7HT UK. (3)Disease Control and Elimination Theme,

Medical Research Council Unit, Fajara, POB273 The Gambia. (4)The Genome

Institute, Washington University, St Louis, MO 63108 USA ; The Jackson Laboratory

for Genomic Medicine, Farmington, CT 06030 USA. (5)Department of Clinical

Research, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK ;

Disease Control and Elimination Theme, Medical Research Council Unit, Fajara,

POB273 The Gambia.


BACKGROUND: Trachoma, caused by Chlamydia trachomatis, remains the world's

leading infectious cause of blindness. Repeated ocular infection during childhood

leads to scarring of the conjunctiva, in-turning of the eyelashes (trichiasis)

and corneal opacity in later life. There is a growing body of evidence to suggest

non-chlamydial bacteria are associated with clinical signs of trachoma,

independent of C. trachomatis infection.

METHODS: We used deep sequencing of the V1-V3 region of the bacterial 16S rRNA

gene to characterize the microbiome of the conjunctiva of 220 residents of The

Gambia, 105 with healthy conjunctivae and 115 with clinical signs of trachoma in

the absence of detectable C. trachomatis infection. Deep sequencing was carried

out using the Roche-454 platform. Sequence data were processed and analyzed

through a pipeline developed by the Human Microbiome Project.

RESULTS: The microbiome of healthy participants was influenced by age and season

of sample collection with increased richness and diversity seen in younger

participants and in samples collected during the dry season. Decreased diversity

and an increased abundance of Corynebacterium and Streptococcus were seen in

participants with conjunctival scarring compared to normal controls. Abundance of

Corynebacterium was higher still in adults with scarring and trichiasis compared

to adults with scarring only.

CONCLUSIONS: Our results indicate that changes in the conjunctival microbiome

occur in trachomatous disease; whether these are a cause or a consequence is yet



DOI: 10.1186/s13073-014-0099-x

PMCID: PMC4256740

PMID: 25484919  [PubMed]



149. Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8. doi:

10.1073/pnas.1002355107. Epub 2010 Apr 2.


Organismal, genetic, and transcriptional variation in the deeply sequenced gut

microbiomes of identical twins.


Turnbaugh PJ(1), Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit

J, Egholm M, Henrissat B, Knight R, Gordon JI.


Author information:

(1)Center for Genome Sciences, Washington University School of Medicine, St

Louis, MO 63108, USA.


We deeply sampled the organismal, genetic, and transcriptional diversity in fecal

samples collected from a monozygotic (MZ) twin pair and compared the results to

1,095 communities from the gut and other body habitats of related and unrelated

individuals. Using a new scheme for noise reduction in pyrosequencing data, we

estimated the total diversity of species-level bacterial phylotypes in the

1.2-1.5 million bacterial 16S rRNA reads obtained from each deeply sampled cotwin

to be approximately 800 (35.9%, 49.1% detected in both). A combined 1.1 million

read 16S rRNA dataset representing 281 shallowly sequenced fecal samples from 54

twin pairs and their mothers contained an estimated 4,018 species-level

phylotypes, with each sample having a unique species assemblage (53.4 +/- 0.6%

and 50.3 +/- 0.5% overlap with the deeply sampled cotwins). Of the 134 phylotypes

with a relative abundance of >0.1% in the combined dataset, only 37 appeared in

>50% of the samples, with one phylotype in the Lachnospiraceae family present in

99%. Nongut communities had significantly reduced overlap with the deeply

sequenced twins' fecal microbiota (18.3 +/- 0.3%, 15.3 +/- 0.3%). The MZ cotwins'

fecal DNA was deeply sequenced (3.8-6.3 Gbp/sample) and assembled reads were

assigned to 25 genus-level phylogenetic bins. Only 17% of the genes in these bins

were shared between the cotwins. Bins exhibited differences in their degree of

sequence variation, gene content including the repertoire of carbohydrate active

enzymes present within and between twins (e.g., predicted cellulases, dockerins),

and transcriptional activities. These results provide an expanded perspective

about features that make each of us unique life forms and directions for future

characterization of our gut ecosystems.


DOI: 10.1073/pnas.1002355107

PMCID: PMC2867707

PMID: 20363958  [PubMed - indexed for MEDLINE]



150. PLoS Pathog. 2008 Feb 8;4(2):e20. doi: 10.1371/journal.ppat.0040020.


The macaque gut microbiome in health, lentiviral infection, and chronic



McKenna P(1), Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady

M, Knight R, Bushman FD.


Author information:

(1)Department of Microbiology, University of Pennsylvania School of Medicine,

Philadelphia, Pennsylvania, United States of America.


The vertebrate gut harbors a vast community of bacterial mutualists, the

composition of which is modulated by the host immune system. Many

gastrointestinal (GI) diseases are expected to be associated with disruptions of

host-bacterial interactions, but relatively few comprehensive studies have been

reported. We have used the rhesus macaque model to investigate forces shaping GI

bacterial communities. We used DNA bar coding and pyrosequencing to characterize

141,000 sequences of 16S rRNA genes obtained from 100 uncultured GI bacterial

samples, allowing quantitative analysis of community composition in health and

disease. Microbial communities of macaques were distinct from those of mice and

humans in both abundance and types of taxa present. The macaque communities

differed among samples from intestinal mucosa, colonic contents, and stool,

paralleling studies of humans. Communities also differed among animals, over time

within individual animals, and between males and females. To investigate changes

associated with disease, samples of colonic contents taken at necropsy were

compared between healthy animals and animals with colitis and undergoing

antibiotic therapy. Communities from diseased and healthy animals also differed

significantly in composition. This work provides comprehensive data and improved

methods for studying the role of commensal microbiota in macaque models of GI

diseases and provides a model for the large-scale screening of the human gut



DOI: 10.1371/journal.ppat.0040020

PMCID: PMC2222957

PMID: 18248093  [PubMed - indexed for MEDLINE]



151. Gut Pathog. 2016 Feb 12;8:3. doi: 10.1186/s13099-016-0087-3. eCollection 2016.


Whole genome sequencing of "Faecalibaculum rodentium" ALO17, isolated from

C57BL/6J laboratory mouse feces.


Lim S(1), Chang DH(1), Ahn S(2), Kim BC(2).


Author information:

(1)Microbiomix and Immunity Research Center, Korea Research Institute of

Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon, 34141

South Korea. (2)Microbiomix and Immunity Research Center, Korea Research

Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu,

Daejeon, 34141 South Korea ; Department of Biosystems and Bioengineering,

University of Science and Technology (UST), 217 Gwahangno, Yuseong-gu, Daejeon,

South Korea.


BACKGROUND: Intestinal microorganisms affect host physiology, including ageing.

Given the difficulty in controlling for human studies of the gut microbiome,

mouse models provide an alternative avenue to study such relationships. In this

study, we report on the complete genome of "Faecalibaculum rodentium" ALO17, a

bacterium that was isolated from the faeces of a 9-month-old female C57BL/6J

mouse. This strain will be utilized in future in vivo studies detailing the

relationships between the gut microbiome and ageing.

RESULTS: The whole genome sequence of "F. rodentium" ALO17 was obtained using

single-molecule, real-time (SMRT) technique on a PacBio instrument. The assembled

genome consisted of 2,542,486 base pairs of double-stranded DNA with a GC content

of 54.0 % and no plasmids. The genome was predicted to contain 2794 open reading

frames, 55 tRNA genes, and 38 rRNA genes. The 16S rRNA gene of ALO17 was 86.9 %

similar to that of Allobaculum stercoricanis DSM 13633(T), and the average

overall nucleotide identity between strains ALO17 and DSM 13633(T) was 66.8 %.

After confirming the phylogenetic relationship between "F. rodentium" ALO17 and

A. stercoricanis DSM 13633(T), their whole genome sequences were compared,

revealing that "F. rodentium" ALO17 contains more fermentation-related genes than

A. stercoricanis DSM 13633(T). Furthermore, "F. rodentium" ALO17 produces higher

levels of lactic acid than A. stercoricanis DSM 13633(T) as determined by

high-performance liquid chromatography.

CONCLUSION: The availability of the "F. rodentium" ALO17 whole genome sequence

will enhance studies concerning the gut microbiota and host physiology,

especially when investigating the molecular relationships between gut microbiota

and ageing.


DOI: 10.1186/s13099-016-0087-3

PMCID: PMC4752744

PMID: 26877770  [PubMed]



152. J Clin Microbiol. 2012 Nov;50(11):3562-8. doi: 10.1128/JCM.00767-12. Epub 2012

Aug 22.


Microbiome diversity in the bronchial tracts of patients with chronic obstructive

pulmonary disease.


Cabrera-Rubio R(1), Garcia-Núñez M, Setó L, Antó JM, Moya A, Monsó E, Mira A.


Author information:

(1)Department of Genomics and Health, Center for Public Health Research,

Valencia, Spain.


Culture of bacteria from bronchial secretions in respiratory patients has low

sensitivity and does not allow for complete assessment of microbial diversity

across different bronchial compartments. In addition, a significant number of

clinical studies are based on sputum samples, and it is not known to what extent

they describe the real diversity of the mucosa. In order to identify previously

unrecognized lower airway bacteria and to investigate the complexity and

distribution of microbiota in patients with chronic obstructive pulmonary disease

(COPD), we performed PCR amplification and pyrosequencing of the 16S rRNA gene in

patients not showing signs or symptoms of infection. Four types of respiratory

samples (sputum, bronchial aspirate, bronchoalveolar lavage, and bronchial

mucosa) were taken from each individual, obtaining on average >1,000 16S rRNA

sequences per sample. The total number of genera per patient was >100, showing a

high diversity, with Streptococcus, Prevotella, Moraxella, Haemophilus,

Acinetobacter, Fusobacterium, and Neisseria being the most commonly identified.

Sputum samples showed significantly lower diversity than the other three sample

types. Lower-bronchial-tree samples, i.e., bronchoalveolar lavage and bronchial

mucosa, showed a very similar bacterial compositions in contrast to sputum and

bronchial aspirate samples. Thus, sputum and bronchial aspirate samples are upper

bronchial tree samples that are not representative of the lower bronchial mucosa

flora, and bronchoalveolar lavage samples showed the results closest to those for

the bronchial mucosa. Our data confirm that the bronchial tree is not sterile in

COPD patients and support the existence a different microbiota in the upper and

lower compartments.


DOI: 10.1128/JCM.00767-12

PMCID: PMC3486223

PMID: 22915614  [PubMed - indexed for MEDLINE]



153. Microbiome. 2014 Feb 24;2(1):6. doi: 10.1186/2049-2618-2-6.


An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on

the Illumina MiSeq platform.


Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J(1).


Author information:

(1)Institute for Genome Sciences, Department of Microbiology and Immunology,

University of Maryland School of Medicine, 801 W, Baltimore Street, Baltimore, MD

21201, USA. jravel@som.umaryland.edu.


BACKGROUND: To take advantage of affordable high-throughput next-generation

sequencing technologies to characterize microbial community composition often

requires the development of improved methods to overcome technical limitations

inherent to the sequencing platforms. Sequencing low sequence diversity libraries

such as 16S rRNA amplicons has been problematic on the Illumina MiSeq platform

and often generates sequences of suboptimal quality.

RESULTS: Here we present an improved dual-indexing amplification and sequencing

approach to assess the composition of microbial communities from clinical samples

using the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform. We

introduced a 0 to 7 bp "heterogeneity spacer" to the index sequence that allows

an equal proportion of samples to be sequenced out of phase.

CONCLUSIONS: Our approach yields high quality sequence data from 16S rRNA gene

amplicons using both 250 bp and 300 bp paired-end MiSeq protocols and provides a

flexible and cost-effective sequencing option.


DOI: 10.1186/2049-2618-2-6

PMCID: PMC3940169

PMID: 24558975  [PubMed]




Association of household siblings with nasal and fecal microbiota in infants.

Hasegawa K1, Linnemann RW2, Mansbach JM3, Ajami NJ4, Espinola JA5, Fiechtner LG6, Petrosino JF4, Camargo CA Jr5.

Author information



Early-life exposure to older siblings is associated with a lower risk of asthma. To date, no study has addressed the impact of having siblings on both the airway and fecal microbiota during infancy. We aimed to profile the nasal airway and fecal microbiota in infants, and to examine the association between having siblings and microbiota profiles.


We conducted a cross-sectional study of 105 healthy infants (aged <1 year). By applying 16S rRNA gene sequencing and an unbiased clustering approach to the nasal airway and fecal samples, we identified microbiota profiles and then determined the association between having siblings and microbiome profiles.


Overall, the median age was 3.4 months (IQR, 2.0-4.7 months); 43% had siblings in the household. Unbiased clustering of nasal airway microbiota identified three profiles: Moraxella-dominant (43%), Corynebacterium/Dolosigranulum-dominant (36%), and mixed (21%). Infants with siblings were more likely to have Moraxella-dominant profile than Corynebacterium/Dolosigranulum-dominant profile (76% vs. 18%) while those without siblings had the opposite pattern (18% vs. 50%) (multivariable-adjusted P<0.001). Fecal microbiota consisted of three profiles: Bifidobacterium-dominant (39%), Escherichia-dominant (31%), and Enterobacter-dominant (30%). Infants with siblings were more likely to have Bifidobacterium-dominant profile than Escherichia-dominant profile (49% vs. 24%) while those without siblings had the opposite pattern (32% vs. 37%) (multivariable-adjusted P=0.04).


In this cross-sectional study, we found that infants with siblings were more likely to have Moraxella-dominant nasal microbiota profile and Bifidobacterium-dominant fecal microbiota profile. Our findings should facilitate further investigation of the interplay between early-life environmental exposures, the microbiome, and childhood asthma. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.


airway microbiota; asthma; fecal microbiota; infants; sibling

PMID: 27638139 DOI: 10.1111/ped.13168

[PubMed - as supplied by publisher]

Similar articles

Icon for Wiley

Select item 27637802




J Ethnopharmacol. 2016 Sep 13. pii: S0378-8741(16)30818-2. doi: 10.1016/j.jep.2016.09.027. [Epub ahead of print]

Qualitatively and Quantitatively Investigating the Regulation of Intestinal Microbiota on the Metabolism of Panax notoginseng saponins.

Xiao J1, Chen H1, Kang D1, Shao Y1, Shen B1, Li X1, Yin X1, Zhu Z1, Li H1, Rao T1, Xie L1, Wang G2, Liang Y2.

Author information



Intestinal microflora plays crucial roles in modulating pharmacokinetic characteristics and pharmacological actions of active ingredients in traditional Chinese medicines (TCMs). However, the exact impact of altered intestinal microflora affecting the biotransformation of TCMs remains poorly understood.


This study aimed to reveal the specific enterobacteria which dominate the metabolism of panax notoginseng saponins (PNSs) via exploring the relationship between bacterial community structures and the metabolic profiles of PNSs.


2, 4, 6-Trinitrobenzenesulphonic acid (TNBS)-challenged and pseudo germ-free (pseudo GF) rats, which prepared by treating TNBS and antibiotic cocktail, respectively, were employed to investigate the influence of intestinal microflora on the PNS metabolic profiles. Firstly, the bacterial community structures of the conventional, TNBS-challenged and pseudo GF rat intestinal microflora were compared via 16S rDNA amplicon sequencing technique. Then, the biotransformation of protopanaxadiol-type PNSs (ginsenoside Rb1, Rb2 and Rd), protopanaxatriol-type PNSs (ginsenoside Re, Rf, Rg1 and notoginsenoside R1) and Panax notoginseng extract (PNE) in conventional, TNBS-challenged and pseudo GF rat intestinal microbiota was systematically studied from qualitative and quantitative angles based on LC-triple-TOF/MS system. Besides, glycosidases (β-glucosidase and β-xylosidase), predominant enzymes responsible for the deglycosylation of PNSs, were measured by the glycosidases assay kits.


Significant differences in the bacterial community structure on phylum, class, order, family, and genera levels were observed among the conventional, TNBS-challenged and pseudo GF rats. Most of the metabolites in TNBS-challenged rat intestinal microflora were identified as the deglycosylation products, and had slightly lower exposure levels than those in the conventional rats. In the pseudo GF group, the peak area of metabolites formed by loss of glucose, xylose and rhamnose was significantly lower than that in the conventional group. Importantly, the exposure levels of the deglycosylated metabolites were found have a high correlation with the alteration of glycosidase activities and proteobacteria population. Several other metabolites, which formed by oxidation, dehydrogenation, demethylation, etc, had higher relative exposure in pseudo GF group, which implicated that the up-regulation of Bacteroidetes could enhance the activities of some redox enzymes in intestinal microbiota.


The metabolism of PNSs was greatly influenced by intestinal microflora. Proteobacteria may affect the deglycosylated metabolism of PNSs via regulating the activities of glycosidases. Besides, up-regulation of Bacteroidetes was likely to promote the redox metabolism of PNSs via improving the activities of redox metabolic enzymes in intestinal microflora.

Copyright © 2016. Published by Elsevier Ireland Ltd.


Deglycosylation; Glycosidase; Intestinal microflora; Panax notoginseng extract; Panax notoginseng saponin

PMID: 27637802 DOI: 10.1016/j.jep.2016.09.027

[PubMed - as supplied by publisher]

Similar articles

Icon for Elsevier Science

Select item 27636701




Eur J Contracept Reprod Health Care. 2016 Sep 16:1-7. [Epub ahead of print]

Neither vaginal nor buccal administration of 800 μg misoprostol alters mucosal and systemic immune activation or the cervicovaginal microbiome: a pilot study.

Kalams SA1, Rogers LM1, Smith RM1, Barnett L1, Crumbo K1, Sumner S1, Prashad N1, Rybczyk K1, Milne G2, Dowd SE3, Chong E4, Winikoff B4, Aronoff DM1.

Author information



The aim of the study was to assess the extent to which misoprostol alters mucosal or systemic immune responses following either buccal or vaginal administration.


This was a prospective, crossover pilot study of 15 healthy, reproductive-age women. Women first received 800 μg misoprostol either via buccal or vaginal administration and were crossed over 1 month later to receive the drug via the other route. Cervicovaginal lavage samples, cervical Cytobrush samples, cervicovaginal swabs, urine and blood were obtained immediately prior to drug administration and the following day. Parameters assessed included urine and cervicovaginal misoprostol levels, whole blood cytokine responses (by ELISA) to immune stimulation with lipopolysaccharide, peripheral blood and cervical lymphocyte phenotyping by flow cytometry, cervicovaginal antimicrobial peptide measurement by ELISA and vaginal microbial ecology assessment by 16S rRNA sequencing.


Neither buccal nor vaginal misoprostol significantly altered local or systemic immune and microbiological parameters.


In this pilot study, we did not observe significant alteration of mucosal or systemic immunology or vaginal microbial ecology 1 day after drug administration following either the buccal or vaginal route.


Abortion; microbial ecology; mucosal immunology; prostaglandins

PMID: 27636701 DOI: 10.1080/13625187.2016.1229765

[PubMed - as supplied by publisher]

Similar articles

Icon for Taylor & Francis

Select item 27635335




PeerJ. 2016 Aug 24;4:e2367. doi: 10.7717/peerj.2367. eCollection 2016.

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species.

Laforest-Lapointe I1, Messier C2, Kembel SW1.

Author information



The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada.


We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1-2 m height), the four cardinal points of mid-canopy (2-4 m height), and the top-canopy (4-6 m height). We also collected bottom-canopy leaves from five additional trees from each species.


Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%).


Our results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome.


Bioindicator; Inter-individual variation; Interspecific variation; Intra-individual variation; Microbiome; Phyllosphere; Plant-bacteria interaction; Temperate forest


What the Naked Eye Can't See with MR DNA!!