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]


121. PLoS One. 2015 Feb 25;10(2):e0118068. doi: 10.1371/journal.pone.0118068.

eCollection 2015.


Biotic stress shifted structure and abundance of Enterobacteriaceae in the

lettuce microbiome.


Erlacher A(1), Cardinale M(1), Grube M(2), Berg G(3).


Author information:

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

Petersgasse 12, 8010, Graz, Austria; Institute of Plant Sciences, University of

Graz, Holteigasse 6, 8010, Graz, Austria. (2)Institute of Plant Sciences,

University of Graz, Holteigasse 6, 8010, Graz, Austria. (3)Institute of

Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010,

Graz, Austria.


Lettuce cultivars are not only amongst the most popular vegetables eaten raw,

they are also involved in severe pathogen outbreaks world-wide. While outbreaks

caused by Enterobacteriaceae species are well-studied, less is known about their

occurrence in natural environments as well as the impact of biotic stress. Here,

we studied the ecology of the human health-relevant bacterial family

Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne

phytopathogenic fungus and Gastropoda on their structure and abundance in

mesocosm and pot experiments. Using a polyphasic approach including network

analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary

fluorescence in situ hybridization (FISH) microscopy we found substantial yet

divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was

identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae

was on average 3fold higher in phyllosphere samples. Both stress factors shifted

the bacterial community of the leaf habitat, characterized by increases of

species abundance and diversity. For the rhizosphere, we observed significant

structural shifts of Enterobacteriaceae communities but also a high degree of

resilience. These results could be confirmed by FISH microscopy but it was

difficult to visualize phyllosphere communities. Additional inoculation

experiments with Escherichia coli as model revealed their presence below the wax

layer as well as in the endosphere of leaves. The observed presence influenced by

stress factors and the endophytic life style of Enterobacteriaceae on lettuce can

be an important aspect in relation to human health.


DOI: 10.1371/journal.pone.0118068

PMCID: PMC4340628

PMID: 25714833  [PubMed - indexed for MEDLINE]



122. PLoS One. 2015 Feb 12;10(2):e0116704. doi: 10.1371/journal.pone.0116704.

eCollection 2015.


Effects of vendor and genetic background on the composition of the fecal

microbiota of inbred mice.


Ericsson AC(1), Davis JW(2), Spollen W(3), Bivens N(4), Givan S(3), Hagan CE(5),

McIntosh M(6), Franklin CL(1).


Author information:

(1)Department of Veterinary Pathobiology, University of Missouri, Columbia,

Missouri, United States of America; Mutant Mouse Resource and Research Center,

University of Missouri, Columbia, Missouri, United States of America; University

of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri,

United States of America. (2)Department of Biostatistics, University of Missouri,

Columbia, Missouri, United States of America. (3)Informatics Research Core

Facility, University of Missouri, Columbia, Missouri, United States of America.

(4)DNA Core Facility, University of Missouri, Columbia, Missouri, United States

of America. (5)Department of Veterinary Pathobiology, University of Missouri,

Columbia, Missouri, United States of America. (6)DNA Core Facility, University of

Missouri, Columbia, Missouri, United States of America; Department of Molecular

Microbiology and Immunology, University of Missouri, Columbia, Missouri, United

States of America.


The commensal gut microbiota has been implicated as a determinant in several

human diseases and conditions. There is mounting evidence that the gut microbiota

of laboratory mice (Mus musculus) similarly modulates the phenotype of mouse

models used to study human disease and development. While differing model

phenotypes have been reported using mice purchased from different vendors, the

composition and uniformity of the fecal microbiota in mice of various genetic

backgrounds from different vendors is unclear. Using culture-independent methods

and robust statistical analysis, we demonstrate significant differences in the

richness and diversity of fecal microbial populations in mice purchased from two

large commercial vendors. Moreover, the abundance of many operational taxonomic

units, often identified to the species level, as well as several higher taxa,

differed in vendor- and strain-dependent manners. Such differences were evident

in the fecal microbiota of weanling mice and persisted throughout the study, to

twenty-four weeks of age. These data provide the first in-depth analysis of the

developmental trajectory of the fecal microbiota in mice from different vendors,

and a starting point from which researchers may be able to refine animal models

affected by differences in the gut microbiota and thus possibly reduce the number

of animals required to perform studies with sufficient statistical power.


DOI: 10.1371/journal.pone.0116704

PMCID: PMC4326421

PMID: 25675094  [PubMed - indexed for MEDLINE]



123. PLoS One. 2016 Feb 9;11(2):e0148534. doi: 10.1371/journal.pone.0148534.

eCollection 2016.


Assessment of the Microbial Constituents of the Home Environment of Individuals

with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections.


Heirali A(1,)(2), McKeon S(1), Purighalla S(1), Storey DG(1,)(2), Rossi L(3),

Costilhes G(1), Drews SJ(4), Rabin HR(1,)(5), Surette MG(1,)(3), Parkins



Author information:

(1)Department of Microbiology Immunology and Infectious Diseases, University of

Calgary, Calgary, AB, Canada. (2)Department of Biological Sciences, University of

Calgary, Calgary, AB, Canada. (3)The Department of Biochemistry & Biomedical

Sciences, McMaster University, Hamilton, ON, Canada. (4)Department of Laboratory

Medicine & Pathology, University of Alberta, Edmonton, AB, Canada. (5)Department

of Medicine, The University of Calgary, Calgary, AB, Canada.


INTRODUCTION: Cystic fibrosis (CF) airways are colonized by a polymicrobial

community of organisms, termed the CF microbiota. We sought to define the

microbial constituents of the home environment of individuals with CF and

determine if it may serve as a latent reservoir for infection.

METHODS: Six patients with newly identified CF pathogens were included. An

investigator collected repeat sputum and multiple environmental samples from

their homes. Bacteria were cultured under both aerobic and anaerobic conditions.

Morphologically distinct colonies were selected, purified and identified to the

genus and species level through 16S rRNA gene sequencing. When concordant

organisms were identified in sputum and environment, pulsed-field gel

electrophoresis (PFGE) was performed to determine relatedness.

Culture-independent bacterial profiling of each sample was carried out by

Illumina sequencing of the V3 region of the 16s RNA gene.

RESULTS: New respiratory pathogens prompting investigation included:

Mycobacterium abscessus(2), Stenotrophomonas maltophilia(3), Pseudomonas

aeruginosa(3), Pseudomonas fluorescens(1), Nocardia spp.(1), and Achromobacter

xylosoxidans(1). A median 25 organisms/patient were cultured from sputum. A

median 125 organisms/home were cultured from environmental sites. Several

organisms commonly found in the CF lung microbiome were identified within the

home environments of these patients. Concordant species included members of the

following genera: Brevibacterium(1), Microbacterium(1), Staphylococcus(3),

Stenotrophomonas(2), Streptococcus(2), Sphingomonas(1), and Pseudomonas(4). PFGE

confirmed related strains (one episode each of Sphinogomonas and P. aeruginosa)

from the environment and airways were identified in two patients.

Culture-independent assessment confirmed that many organisms were not identified

using culture-dependent techniques.

CONCLUSIONS: Members of the CF microbiota can be found as constituents of the

home environment in individuals with CF. While the majority of isolates from the

home environment were not genetically related to those isolated from the lower

airways of individuals with CF suggesting alternate sources of infection were

more common, a few genetically related isolates were indeed identified. As such,

the home environment may rarely serve as either the source of infection or a

persistent reservoir for re-infection after clearance.


DOI: 10.1371/journal.pone.0148534

PMCID: PMC4747485

PMID: 26859493  [PubMed - indexed for MEDLINE]



124. BMC Genomics. 2014 Apr 5;15:266. doi: 10.1186/1471-2164-15-266.


The intestinal microbiome of fish under starvation.


Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, Liu XJ, Yue GH(1).


Author information:

(1)Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1

Research Link, National University of Singapore, Singapore 117604, Republic of

Singapore. genhua@tll.org.sg.


BACKGROUND: Starvation not only affects the nutritional and health status of the

animals, but also the microbial composition in the host's intestine.

Next-generation sequencing provides a unique opportunity to explore gut microbial

communities and their interactions with hosts. However, studies on gut

microbiomes have been conducted predominantly in humans and land animals. Not

much is known on gut microbiomes of aquatic animals and their changes under

changing environmental conditions. To address this shortcoming, we determined the

microbial gene catalogue, and investigated changes in the microbial composition

and host-microbe interactions in the intestine of Asian seabass in response to


RESULTS: We found 33 phyla, 66 classes, 130 orders and 278 families in the

intestinal microbiome. Proteobacteria (48.8%), Firmicutes (15.3%) and

Bacteroidetes (8.2%) were the three most abundant bacteria taxa. Comparative

analyses of the microbiome revealed shifts in bacteria communities, with dramatic

enrichment of Bacteroidetes, but significant depletion of Betaproteobacteria in

starved intestines. In addition, significant differences in clusters of

orthologous groups (COG) functional categories and orthologous groups were

observed. Genes related to antibiotic activity in the microbiome were

significantly enriched in response to starvation, and host genes related to the

immune response were generally up-regulated.

CONCLUSIONS: This study provides the first insights into the fish intestinal

microbiome and its changes under starvation. Further detailed study on

interactions between intestinal microbiomes and hosts under dynamic conditions

will shed new light on how the hosts and microbes respond to the changing



DOI: 10.1186/1471-2164-15-266

PMCID: PMC4234480

PMID: 24708260  [PubMed - indexed for MEDLINE]



125. J Natl Cancer Inst. 2015 Jun 1;107(8). pii: djv147. doi: 10.1093/jnci/djv147.

Print 2015 Aug.


Investigation of the association between the fecal microbiota and breast cancer

in postmenopausal women: a population-based case-control pilot study.


Goedert JJ(1), Jones G(2), Hua X(2), Xu X(2), Yu G(2), Flores R(2), Falk RT(2),

Gail MH(2), Shi J(2), Ravel J(2), Feigelson HS(2).


Author information:

(1)Division of Cancer Epidemiology and Genetics (JJG, GJ, XH, GY, RF, RTF, MHG,

JS) and Division of Cancer Prevention (RF), National Cancer Institute, Bethesda,

MD; Cancer Research Technology Program, Leidos Biomedical Research, Inc.,

Frederick National Laboratory for Cancer Research, Frederick, MD (XX); Institute

for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD

(JR); Institute for Health Research, Kaiser Permanente Colorado, Denver, CO

(HSF). goedertj@mail.nih.gov. (2)Division of Cancer Epidemiology and Genetics

(JJG, GJ, XH, GY, RF, RTF, MHG, JS) and Division of Cancer Prevention (RF),

National Cancer Institute, Bethesda, MD; Cancer Research Technology Program,

Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer

Research, Frederick, MD (XX); Institute for Genome Sciences, University of

Maryland School of Medicine, Baltimore, MD (JR); Institute for Health Research,

Kaiser Permanente Colorado, Denver, CO (HSF).


We investigated whether the gut microbiota differed in 48 postmenopausal breast

cancer case patients, pretreatment, vs 48 control patients. Microbiota profiles

in fecal DNA were determined by Illumina sequencing and taxonomy of 16S rRNA

genes. Estrogens were quantified in urine. Case-control comparisons employed

linear and unconditional logistic regression of microbiota α-diversity (PD_whole

tree) and UniFrac analysis of β-diversity, with two-sided statistical tests.

Total estrogens correlated with α-diversity in control patients (Spearman Rho =

0.37, P = .009) but not case patients (Spearman Rho = 0.04, P = .77). Compared

with control patients, case patients had statistically significantly altered

microbiota composition (β-diversity, P = .006) and lower α-diversity (P = .004).

Adjusted for estrogens and other covariates, odds ratio of cancer was 0.50 (95%

confidence interval = 0.30 to 0.85) per α-diversity tertile. Differences in

specific taxa were not statistically significant when adjusted for multiple

comparisons. This pilot study shows that postmenopausal women with breast cancer

have altered composition and estrogen-independent low diversity of their gut

microbiota. Whether these affect breast cancer risk and prognosis is unknown.


Published by Oxford University Press 2015. This work is written by (a) US

Government employee(s) and is in the public domain in the US.


DOI: 10.1093/jnci/djv147

PMCID: PMC4554191

PMID: 26032724  [PubMed - indexed for MEDLINE]



126. PLoS One. 2015 Jul 28;10(7):e0132892. doi: 10.1371/journal.pone.0132892.

eCollection 2015.


Characterization of Antibiotic Resistance Gene Abundance and Microbiota

Composition in Feces of Organic and Conventional Pigs from Four EU Countries.


Gerzova L(1), Babak V(1), Sedlar K(2), Faldynova M(1), Videnska P(1), Cejkova

D(1), Jensen AN(3), Denis M(4), Kerouanton A(4), Ricci A(5), Cibin V(5),

Österberg J(6), Rychlik I(1).


Author information:

(1)Veterinary Research Institute, Brno, Czech Republic. (2)Brno University of

Technology, Brno, Czech Republic. (3)Technical University of Denmark, National

Food Institute, Copenhagen, Denmark. (4)Anses, Hygiene and Quality of Poultry and

Pig Products Unit, Ploufragan, France. (5)Istituto Zooprofilattico Sperimentale

delle Venezie, Padova, Italy. (6)National Veterinary Institute (SVA), Uppsala,



One of the recent trends in animal production is the revival of interest in

organic farming. The increased consumer interest in organic animal farming is

mainly due to concerns about animal welfare and the use of antibiotics in

conventional farming. On the other hand, providing animals with a more natural

lifestyle implies their increased exposure to environmental sources of different

microorganisms including pathogens. To address these concerns, we determined the

abundance of antibiotic resistance and diversity within fecal microbiota in pigs

kept under conventional and organic farming systems in Sweden, Denmark, France

and Italy. The abundance of sul1, sul2, strA, tet(A), tet(B) and cat antibiotic

resistance genes was determined in 468 samples by real-time PCR and the fecal

microbiota diversity was characterized in 48 selected samples by pyrosequencing

of V3/V4 regions of 16S rRNA. Contrary to our expectations, there were no

extensive differences between the abundance of tested antibiotic resistance genes

in microbiota originating from organic or conventionally housed pigs within

individual countries. There were also no differences in the microbiota

composition of organic and conventional pigs. The only significant difference was

the difference in the abundance of antibiotic resistance genes in the samples

from different countries. Fecal microbiota in the samples originating from

southern European countries (Italy, France) exhibited significantly higher

antibiotic resistance gene abundance than those from northern parts of Europe

(Denmark, Sweden). Therefore, the geographical location of the herd influenced

the antibiotic resistance in the fecal microbiota more than farm's status as

organic or conventional.


DOI: 10.1371/journal.pone.0132892

PMCID: PMC4517930

PMID: 26218075  [PubMed - indexed for MEDLINE]



127. PLoS One. 2014 Apr 18;9(4):e95476. doi: 10.1371/journal.pone.0095476. eCollection



Short-term effect of antibiotics on human gut microbiota.


Panda S(1), El khader I(1), Casellas F(2), López Vivancos J(3), García Cors M(3),

Santiago A(1), Cuenca S(1), Guarner F(2), Manichanh C(2).


Author information:

(1)Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona,

Spain. (2)Digestive System Research Unit, Vall d'Hebron Research Institute,

Barcelona, Spain; Centro de Investigación Biomédica en Red en el Área temática de

Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III,

Madrid, Spain. (3)Internal Medicine Department, Capio Hospital General de

Catalunya, Universitat Internacional de Catalunya, Barcelona, Spain.


From birth onwards, the human gut microbiota rapidly increases in diversity and

reaches an adult-like stage at three years of age. After this age, the

composition may fluctuate in response to external factors such as antibiotics.

Previous studies have shown that resilience is not complete months after

cessation of the antibiotic intake. However, little is known about the short-term

effects of antibiotic intake on the gut microbial community. Here we examined the

load and composition of the fecal microbiota immediately after treatment in 21

patients, who received broad-spectrum antibiotics such as fluoroquinolones and

β-lactams. A fecal sample was collected from all participants before treatment

and one week after for microbial load and community composition analyses by

quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively.

Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25%

and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the

phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio

(p = 0.0007, FDR = 0.002). At the species level, our findings unexpectedly

revealed that both antibiotic types increased the proportion of several unknown

taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria

(p = 0.0003, FDR<0.016). Furthermore, the average microbial load was affected by

the treatment. Indeed, the β-lactams increased it significantly by two-fold

(p = 0.04). The maintenance of or possible increase detected in microbial load

and the selection of Gram-negative over Gram-positive bacteria breaks the idea

generally held about the effect of broad-spectrum antibiotics on gut microbiota.


DOI: 10.1371/journal.pone.0095476

PMCID: PMC3991704

PMID: 24748167  [PubMed - indexed for MEDLINE]



128. Emerg Infect Dis. 2015 Feb;21(2):242-50. doi: 10.3201/eid2101.140795.


Microbiota that affect risk for shigellosis in children in low-income countries.


Lindsay B, Oundo J, Hossain MA, Antonio M, Tamboura B, Walker AW, Paulson JN,

Parkhill J, Omore R, Faruque AS, Das SK, Ikumapayi UN, Adeyemi M, Sanogo D, Saha

D, Sow S, Farag TH, Nasrin D, Li S, Panchalingam S, Levine MM, Kotloff K, Magder

LS, Hungerford L, Sommerfelt H, Pop M, Nataro JP, Stine OC.


Pathogens in the gastrointestinal tract exist within a vast population of

microbes. We examined associations between pathogens and composition of gut

microbiota as they relate to Shigella spp./enteroinvasive Escherichia coli

infection. We analyzed 3,035 stool specimens (1,735 nondiarrheal and 1,300

moderate-to-severe diarrheal) from the Global Enteric Multicenter Study for 9

enteropathogens. Diarrheal specimens had a higher number of enteropathogens

(diarrheal mean 1.4, nondiarrheal mean 0.95; p<0.0001). Rotavirus showed a

negative association with Shigella spp. in cases of diarrhea (odds ratio 0.31,

95% CI 0.17-0.55) and had a large combined effect on moderate-to-severe diarrhea

(odds ratio 29, 95% CI 3.8-220). In 4 Lactobacillus taxa identified by 16S rRNA

gene sequencing, the association between pathogen and disease was decreased,

which is consistent with the possibility that Lactobacillus spp. are protective

against Shigella spp.-induced diarrhea. Bacterial diversity of gut microbiota was

associated with diarrhea status, not high levels of the Shigella spp. ipaH gene.


DOI: 10.3201/eid2101.140795

PMCID: PMC4313639

PMID: 25625766  [PubMed - indexed for MEDLINE]





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!!