mr dna and 16s microbiome sequencing Harvesting Microbial Diversity
A Closer Look At The BeesWax of 16s rRNA Sequencing

 

 

 

 

MR DNA sequencing 16s microbiome, metagenome and more

 

 

161. J Clin Gastroenterol. 2014 Nov-Dec;48 Suppl 1:S28-31. doi:

10.1097/MCG.0000000000000229.

 

Gut microbiota, host gene expression, and aging.

 

Patrignani P(1), Tacconelli S, Bruno A.

 

Author information:

(1)Department of Neuroscience and Imaging, Section of Cardiovascular and

Pharmacological Sciences, Center of Excellence on Aging (CeSI), "G. d'Annunzio"

University, Chieti, Italy.

 

Novel concepts of disease susceptibility and development suggest an important

role of gastrointestinal microbiota and microbial pathogens. They can contribute

to physiological systems and disease processes, even outside of the

gastrointestinal tract. There is increasing evidence that genetics of the host

influence and interact with gut microbiota. Moreover, aging-associated oxidative

stress may cause morphologic alterations of bacterial cells, thus influencing the

aggressive potential and virulence markers of an anaerobic bacterium and finally

the type of interaction with the host. At the same time, microbiota may influence

host gene expression and it is becoming apparent that it may occur through the

regulation of microRNAs. They are short single-stranded noncoding RNAs that

regulate posttranscriptional gene expression by affecting mRNA stability and/or

translational repression of their target mRNAs. The introduction of -omics

approaches (such as metagenomics, metaproteomics, and metatranscriptomics) in

microbiota research will certainly advance our knowledge of this area. This will

lead to greatly deepen our understanding of the molecular targets in the

homeostatic interaction between the gut microbiota and the host and, thereby,

promises to reveal new ways to treat diseases and maintain health.

 

DOI: 10.1097/MCG.0000000000000229

PMID: 25291121  [PubMed - indexed for MEDLINE]

 

 

162. Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11.

 

Diet rapidly and reproducibly alters the human gut microbiome.

 

David LA(1), Maurice CF(2), Carmody RN(2), Gootenberg DB(2), Button JE(2), Wolfe

BE(2), Ling AV(3), Devlin AS(4), Varma Y(4), Fischbach MA(4), Biddinger SB(3),

Dutton RJ(2), Turnbaugh PJ(2).

 

Author information:

(1)1] FAS Center for Systems Biology, Harvard University, Cambridge,

Massachusetts 02138, USA [2] Society of Fellows, Harvard University, Cambridge,

Massachusetts 02138, USA [3] Molecular Genetics & Microbiology and Institute for

Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA.

(2)FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts

02138, USA. (3)Division of Endocrinology, Children's Hospital Boston, Harvard

Medical School, Boston, Massachusetts 02115, USA. (4)Department of Bioengineering

& Therapeutic Sciences and the California Institute for Quantitative Biosciences,

University of California, San Francisco, San Francisco, California 94158, USA.

 

Comment in

    Nat Biotechnol. 2014 Mar;32(3):243-5.

 

Long-term dietary intake influences the structure and activity of the trillions

of microorganisms residing in the human gut, but it remains unclear how rapidly

and reproducibly the human gut microbiome responds to short-term macronutrient

change. Here we show that the short-term consumption of diets composed entirely

of animal or plant products alters microbial community structure and overwhelms

inter-individual differences in microbial gene expression. The animal-based diet

increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and

Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant

polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii).

Microbial activity mirrored differences between herbivorous and carnivorous

mammals, reflecting trade-offs between carbohydrate and protein fermentation.

Foodborne microbes from both diets transiently colonized the gut, including

bacteria, fungi and even viruses. Finally, increases in the abundance and

activity of Bilophila wadsworthia on the animal-based diet support a link between

dietary fat, bile acids and the outgrowth of microorganisms capable of triggering

inflammatory bowel disease. In concert, these results demonstrate that the gut

microbiome can rapidly respond to altered diet, potentially facilitating the

diversity of human dietary lifestyles.

 

DOI: 10.1038/nature12820

PMCID: PMC3957428

PMID: 24336217  [PubMed - indexed for MEDLINE]

 

 

163. J Appl Genet. 2014 Feb;55(1):145-54. doi: 10.1007/s13353-013-0179-4. Epub 2013

Oct 18.

 

Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high

feed conversion ratio (FCR) broilers.

 

Singh KM(1), Shah TM, Reddy B, Deshpande S, Rank DN, Joshi CG.

 

Author information:

(1)Department of Animal Biotechnology, Anand Agriculture University, Anand,

388001, India, kmsingh18@gmail.com.

 

Individual weight gain in broiler growers appears to vary, which may in part be

due to variation in their gut microbiota. In this paper we analyse the fecal

microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun

sequencing of the fecal microbiome, we used the SEED database to identify the

microbial diversity and metabolic potential in low and high FCR birds. The

domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %),

archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria

(78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 %

in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR)

predominated in the fecal microbial community. Poultry fecal metagenomes revealed

the sequences related to 33 genera in both low and high FCR with significantly

different proportion. Functional analysis revealed that genes for the metabolism

of carbohydrates, amino acids and derivatives and protein metabolism were most

abundant in SEED subsystem in both samples. Genes associated with stress,

virulence, cell wall and cell capsule were also abundant. Indeed, genes

associated with sulphur assimilation, flagellum and flagellar motility were over

represented in low FCR birds. This information could help in developing

strategies to improve feed efficiency and feed formulation for broiler chickens.

 

DOI: 10.1007/s13353-013-0179-4

PMID: 24136777  [PubMed - indexed for MEDLINE]

 

 

164. Schizophr Bull. 2015 Sep;41(5):1153-61. doi: 10.1093/schbul/sbu197. Epub 2015 Feb

9.

 

Metagenomic Sequencing Indicates That the Oropharyngeal Phageome of Individuals

With Schizophrenia Differs From That of Controls.

 

Yolken RH(1), Severance EG(2), Sabunciyan S(2), Gressitt KL(2), Chen O(2),

Stallings C(2), Origoni A(3), Katsafanas E(3), Schweinfurth LA(3), Savage CL(3),

Banis M(3), Khushalani S(3), Dickerson FB(3).

 

Author information:

(1)Stanley Laboratory of Developmental Neurovirology, Department of Pediatrics,

Johns Hopkins School of Medicine, Baltimore, MD; rhyolken@gmail.com. (2)Stanley

Laboratory of Developmental Neurovirology, Department of Pediatrics, Johns

Hopkins School of Medicine, Baltimore, MD; (3)Stanley Research Program, Sheppard

Pratt Health System, Baltimore, MD.

 

Mucosal sites such as the oropharynx contain a wide range of microorganisms,

collectively designated as the microbiome. The microbiome can affect behavior

through a number of neurobiological and immunological mechanisms. Most previous

studies have focused on the bacterial components of the microbiome. However, the

microbiome also includes viruses such as bacteriophages, which are viruses that

infect bacteria and alter their metabolism and replication. We employed

metagenomic analysis to characterize bacteriophage genomes in the oral pharynx of

41 individuals with schizophrenia and 33 control individuals without a

psychiatric disorder. This analysis was performed by the generation of more than

100,000,000 sequence reads from each sample and the mapping of these reads to

databases. We identified 79 distinct bacteriophage sequences in the oropharyngeal

samples. Of these, one bacteriophage genome, Lactobacillus phage phiadh, was

found to be significantly different in individuals with schizophrenia (P <

.00037, q < 0.03 adjusted for multiple comparisons). The differential levels of

Lactobacillus phage phiadh remained significant when controlling for age, gender,

race, socioeconomic status, or cigarette smoking (P < .006). Within the group of

individuals with schizophrenia, the level of Lactobacillus phage phiadh

correlated with the prevalence of immunological disorders as well as with the

administration of valproate, which has been shown in animal models to alter the

microbiome. The bacteriophage composition of the oropharynx in individuals with

schizophrenia differs from that of controls. The biological consequences of this

difference and the potential effects of altering bacteriophage levels through

therapeutic interventions are worthy of further investigation.

 

© The Author 2015. Published by Oxford University Press on behalf of the Maryland

Psychiatric Research Center. All rights reserved. For permissions, please email:

journals.permissions@oup.com.

 

DOI: 10.1093/schbul/sbu197

PMCID: PMC4535630

PMID: 25666826  [PubMed - indexed for MEDLINE]

 

 

165. J Antimicrob Chemother. 2014 Oct;69(10):2878-80. doi: 10.1093/jac/dku201. Epub

2014 Jun 12.

 

An emerging understanding of the Janus face of the human microbiome: enhancement

versus impairment of cancer therapy.

 

Vande Voorde J(1), Balzarini J(2), Liekens S(1).

 

Author information:

(1)Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, blok

x-bus 1030, B-3000 Leuven, Belgium. (2)Rega Institute for Medical Research, KU

Leuven, Minderbroedersstraat 10, blok x-bus 1030, B-3000 Leuven, Belgium

jan.balzarini@rega.kuleuven.be.

 

DOI: 10.1093/jac/dku201

PMID: 24925896  [PubMed - indexed for MEDLINE]

 

 

166. Curr Opin Pediatr. 2015 Aug;27(4):496-501. doi: 10.1097/MOP.0000000000000234.

 

Influence of the human intestinal microbiome on obesity and metabolic

dysfunction.

 

Tilg H(1), Adolph TE.

 

Author information:

(1)Department of Internal Medicine I, Gastroenterology, Endocrinology &

Metabolism, Medical University Innsbruck, Innsbruck, Austria.

 

PURPOSE OF REVIEW: Recent studies have suggested that there may be a strong link

between the gut microbiota, energy extraction and body metabolism.

RECENT FINDINGS: Evidence is accumulating that the intestinal microbiota, in

addition to other major factors such as diet and host genetics, contributes to

obesity, metabolic dysfunction and diabetes. Both preclinical experimental and

human studies have shown that obesity and metabolic dysfunction are characterized

by a profound dysbiosis. Several human metagenome-wide association studies have

demonstrated highly significant correlations of certain members of intestinal

microbiota with obesity and type 2 diabetes. In addition dietary factors that

substantially affect microbial composition, microbiota disruption, and the

consequence of early-life antibiotic use, may contribute to childhood obesity and

metabolic dysfunction. Further evidence for an association between microbiota and

metabolic dysfunction has been derived from studies in pregnancy demonstrating

that major gut microbial shifts occur during pregnancy thereby affecting host

metabolism. In particular, the high rate of obesity following caesarean section

could be partially explained by functional alterations in the intestinal

microbiota.

SUMMARY: Obesity and associated metabolic dysfunction emerge from disturbed

interactions between the intestinal microbiota, dietary changes and host immune

functions. A better understanding of this relationship might lead to better

therapies for human metabolic and inflammatory diseases in the future.

 

DOI: 10.1097/MOP.0000000000000234

PMID: 26087428  [PubMed - indexed for MEDLINE]

 

 

167. APMIS. 2015 May;123(5):427-32. doi: 10.1111/apm.12363. Epub 2015 Apr 6.

 

Analysis of microbiota in stable patients with chronic obstructive pulmonary

disease.

 

Aguirre E(1), Galiana A, Mira A, Guardiola R, Sánchez-Guillén L, Garcia-Pachon E,

Santibañez M, Royo G, Rodríguez JC.

 

Author information:

(1)Section of Microbiology, Hospital General Universitario de Elche, Alicante,

Spain.

 

To identify the bacterial diversity (microbiota) in expectorated sputum, a

pyrosequencing method that investigates complex microbial communities of

expectorated sputum was done in 19 stable chronic obstructive pulmonary disease

patients (mean (SD) FEV1: 47 (18%) of predicted value). Using conventional

culture, 3 phyla and 20 bacterial genera were identified, whereas the

pyrosequencing approach detected 9 phyla and 43 genera (p < 0.001). In sputum the

prevalent genera with pyrosequencing approach were Streptococcus, Actinomyces,

Neisseria, Haemophilus, Rothia, Fusobacterium, Gemella, Granulicatella,

Porphyromonas, Prevotella and Veillonella. Enterobacteriaceae, detected

frequently in conventional culture, were not significantly detected with

pyrosequencing methods. In addition, we found that important pathogens such as

Haemophilus and Moraxella were detected more frequently with the new genetic

procedures. The presence of Enterobacteriaceae is probably overestimated with

conventional culture, whereas other difficult cultivable pathogens are

underestimated. These studies open a new perspective for evaluating the role of

bacterial colonization in chronic obstructive pulmonary disease pathogenesis and

progression.

 

© 2015 APMIS. Published by John Wiley & Sons Ltd.

 

DOI: 10.1111/apm.12363

PMID: 25858184  [PubMed - indexed for MEDLINE]

 

 

168. Am J Clin Nutr. 2015 Jan;101(1):55-64. doi: 10.3945/ajcn.114.092064. Epub 2014

Nov 12.

 

Fiber supplementation influences phylogenetic structure and functional capacity

of the human intestinal microbiome: follow-up of a randomized controlled trial.

 

Holscher HD(1), Caporaso JG(1), Hooda S(1), Brulc JM(1), Fahey GC Jr(1), Swanson

KS(1).

 

Author information:

(1)From the Department of Animal Sciences and Division of Nutritional Sciences,

University of Illinois, Urbana, IL (HDH, SH, GCF, and KSS); the Department of

Biological Sciences and Computer Sciences, Northern Arizona University,

Flagstaff, AZ (JGC); and General Mills Inc., Bell Institute of Health and

Nutrition, Minneapolis, MN (JMB).

 

Comment in

    Am J Clin Nutr. 2015 Jan;101(1):1-2.

 

BACKGROUND: In our published randomized, double-blind, placebo-controlled,

3-period crossover trial, healthy adult men (n = 21) consumed bars containing no

supplemental fiber (placebo; NFC), polydextrose (21 g/d), and soluble corn fiber

(SCF; 21 g/d) for 21 d each. Fecal specimens were collected between days 16 and

21 for fermentative end-product analysis and 16S ribosomal RNA bacterial gene

amplification for bacterial taxa identification. Fiber supplementation decreased

fecal putrefaction compounds and shifted abundances of several bacterial taxa.

OBJECTIVE: The objective was to perform whole-genome shotgun 454 pyrosequencing

on the same fecal specimens collected in that clinical trial to obtain

comprehensive fecal bacterial genome sequencing coverage and explore the full

range of bacterial genetic information in the fecal microbiome, thereby using a

systematic approach to study the impact of dietary fiber supplementation on fecal

metabolites, bacterial taxa, and bacterial metagenomes.

DESIGN: Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing

to identify both fecal bacterial populations present and their functional genetic

capacity.

RESULTS: Whole-genome shotgun sequencing results revealed that fiber consumption

shifted the Bacteroidetes:Firmicutes ratio, increasing the relative abundance of

Bacteroidetes 12 ± 2% and 13 ± 2% with polydextrose and SCF, respectively,

compared with NFC. Bivariate correlations showed a positive correlation between

the Bacteroidetes:Firmicutes ratio and total dietary fiber intake but not body

mass index. Principal coordinates analysis of Bray-Curtis distances indicated

that bacterial gene composition was more similar in participants consuming fibers

(polydextrose and SCF combined) in comparison with NFC. Shifts in bacterial gene

abundances after polydextrose and SCF supplementation included genes associated

with carbohydrate, amino acid, and lipid metabolism, as well as metabolism of

cofactors and vitamins.

CONCLUSION: This study conveys novel information about the impact of dietary

fiber supplementation on the phylogenetic structure and functional capacity of

the fecal microbiome of healthy adults.

 

© 2015 American Society for Nutrition.

 

DOI: 10.3945/ajcn.114.092064

PMID: 25527750  [PubMed - indexed for MEDLINE]

 

 

169. Reprod Sci. 2014 Jan;21(1):32-40. doi: 10.1177/1933719113488838. Epub 2013 May

28.

 

Diversity of the vaginal microbiome correlates with preterm birth.

 

Hyman RW(1), Fukushima M, Jiang H, Fung E, Rand L, Johnson B, Vo KC, Caughey AB,

Hilton JF, Davis RW, Giudice LC.

 

Author information:

(1)1Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.

 

Reproductive tract infection is a major initiator of preterm birth (PTB). The

objective of this prospective cohort study of 88 participants was to determine

whether PTB correlates with the vaginal microbiome during pregnancy. Total DNA

was purified from posterior vaginal fornix swabs during gestation. The 16S

ribosomal RNA gene was amplified using polymerase chain reaction primers,

followed by chain-termination sequencing. Bacteria were identified by comparing

contig consensus sequences with the Ribosomal Database Project. Dichotomous

responses were summarized via proportions and continuous variables via means ±

standard deviation. Mean Shannon Diversity index differed by Welch t test (P =

.00016) between caucasians with PTB and term gestation. Species diversity was

greatest among African Americans (P = .0045). Change in microbiome/Lactobacillus

content and presence of putative novel/noxious bacteria did not correlate with

PTB. We conclude that uncultured vaginal bacteria play an important role in PTB

and race/ethnicity and sampling location are important determinants of the

vaginal microbiome.

 

DOI: 10.1177/1933719113488838

PMCID: PMC3857766

PMID: 23715799  [PubMed - indexed for MEDLINE]

 

 

170. Gut Microbes. 2015;6(3):161-72. doi: 10.1080/19490976.2015.1039223.

 

Gut microbiome compositional and functional differences between tumor and

non-tumor adjacent tissues from cohorts from the US and Spain.

 

Allali I(1), Delgado S, Marron PI, Astudillo A, Yeh JJ, Ghazal H, Amzazi S, Keku

T, Azcarate-Peril MA.

 

Author information:

(1)a Department of Cell Biology and Physiology, and Microbiome Core Facility;

University of North Carolina School of Medicine ; Chapel Hill , NC , USA.

 

Colorectal cancer (CRC) is the third most common cancer in the world and the

second leading cause of cancer deaths in the US and Spain. The molecular

mechanisms involved in the etiology of CRC are not yet elucidated due in part to

the complexity of the human gut microbiota. In this study, we compared the

microbiome composition of 90 tumor and matching adjacent tissue (adjacent) from

cohorts from the US and Spain by 16S rRNA amplicon sequencing in order to

determine the impact of the geographic origin on the CRC microbiome. Data showed

a significantly (P < 0.05) higher Phylogenetic Diversity (PD) for the US (PD

Adjacent = 26.3 ± 5.3, PD Tumor = 23.3 ± 6.2) compared to the Spanish cohort (PD

Adjacent = 18.9 ± 5.9, PD Tumor = 18.7 ± 6.6) while no significant differences in

bacterial diversity were observed between tumor and adjacent tissues for

individuals from the same country. Adjacent tissues from the Spanish cohort were

enriched in Firmicutes (SP = 43.9% and US = 22.2%, P = 0.0001) and Actinobacteria

(SP = 1.6% and US = 0.5%, P = 0.0018) compared to US adjacent tissues, while

adjacent tissues from the US had significantly higher abundances of Fusobacteria

(US = 8.1% and SP = 1.5%, P = 0.0023) and Sinergistetes (US = 0.3% and SP = 0.1%,

P = 0.0097). Comparisons between tumor and adjacent tissues in each cohort

identified the genus Eikenella significantly over represented in US tumors (T =

0.024% and A = 0%, P = 0.03), and the genera Fusobacterium (T = 10.4% and A =

1.5%, P = <0.0001), Bulleida (T = 0.36% and A = 0.09%, P = 0.02), Gemella (T =

1.46% and A = 0.19%, P = 0.03), Parvimonas (T = 3.14% and A = 0.86%, P = 0.03),

Campylobacter (T = 0.15% and A = 0.008%, P = 0.047), and Streptococcus (T = 2.84%

and A = 2.19%, P = 0.05) significantly over represented in Spanish tumors.

Predicted metagenome functional content from 16S rRNA surveys showed that

bacterial motility proteins and proteins involved in flagellar assembly were over

represented in adjacent tissues of both cohorts, while pathways involved in fatty

acid biosynthesis, the MAPK signaling pathway, and bacterial toxins were over

represented in tumors. Our study suggests that microbiome compositional and

functional dissimilarities by geographic location should be taken in

consideration when approaching CRC therapeutic options.

 

DOI: 10.1080/19490976.2015.1039223

PMCID: PMC4615176

PMID: 25875428  [PubMed - indexed for MEDLINE]

 

 

171. Microbiome. 2015 Aug 12;3:33. doi: 10.1186/s40168-015-0092-7. eCollection 2015.

 

Collection media and delayed freezing effects on microbial composition of human

stool.

 

Flores R(1), Shi J(2), Yu G(3), Ma B(4), Ravel J(4), Goedert JJ(3), Sinha R(5).

 

Author information:

(1)Nutritional Science Research Group, Division of Cancer Prevention, National

Cancer Institute, National Institutes of Health, 9609 Medical Center Dr.

RM5E554-MSC9788, Bethesda, MD 20892 USA. (2)Biostatistics Branch, Division of

Cancer Epidemiology and Genetics, NCI/NIH, Bethesda, MD USA. (3)Infections and

Immunoepidemiology Branch DCEG/NCI/NIH, Bethesda, MD USA. (4)Institute of Genome

Sciences, University of Maryland School of Medicine, Baltimore, MD USA.

(5)Nutritional Epidemiology Branch, DCEG/NCI/NIH, Bethesda, MD USA.

 

BACKGROUND: Different bacteria in stool have markedly varied growth and survival

when stored at ambient temperature. It is paramount to develop optimal

biostabilization of stool samples during collection and assess long-term storage

for clinical specimens and epidemiological microbiome studies. We evaluated the

effect of collection media and delayed freezing up to 7 days on microbial

composition. Ten participants collected triplicate stool samples each into no

media as well as RNAlater® with and without kanamycin or ciprofloxacin. For each

set of conditions, triplicate samples were frozen on dry ice immediately (time =

0) or frozen at -80 °C after 3-days and 7-days incubation at 25 °C. Microbiota

metrics were estimated from Illumina MiSeq sequences of 16S rRNA gene fragments

(V3-V4 region). Intraclass correlation coefficients (ICC) across triplicates,

collection media, and incubation time were estimated for taxonomy and alpha and

beta diversity metrics.

RESULTS: RNAlater® alone yielded the highest ICCs for diversity metrics at time =

0 [ICC median 0.935 (range 0.89-0.97)], but ICCs varied greatly (range 0.44-1.0)

for taxa with relative abundances <1%. The 3- and 7-day freezing delays were

generally associated with stable beta diversity for all three media conditions.

Freezing delay caused increased variance for Shannon index (median ICC 0.77) and

especially for observed species abundance (median ICC 0.47). Variance in observed

species abundance and in phylogenetic distance whole tree was similarly increased

with a 7-day delay. Antibiotics did not mitigate variance. No media had inferior

ICCs at time 0 and differed markedly from any media in microbiome composition

(e.g., P =0.01 for relative abundance of Bacteroidetes).

CONCLUSION: Bacterial community composition was stable for 7 days at room

temperature in RNAlater® alone. RNAlater® provides some stability for beta

diversity analyses, but analyses of rare taxa will be inaccurate if specimens are

not frozen immediately. RNAlater® could be used as collection media with minimal

change in the microbiota composition.

 

DOI: 10.1186/s40168-015-0092-7

PMCID: PMC4534027

PMID: 26269741  [PubMed - indexed for MEDLINE]

 

 

172. ISME J. 2016 Feb;10(2):321-32. doi: 10.1038/ismej.2015.114. Epub 2015 Aug 14.

 

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that

accelerates diabetes in NOD mice.

 

Brown K(1), Godovannyi A(1), Ma C(2), Zhang Y(3), Ahmadi-Vand Z(1), Dai C(1),

Gorzelak MA(1), Chan Y(1), Chan JM(2), Lochner A(2), Dutz JP(3), Vallance BA(2),

Gibson DL(1).

 

Author information:

(1)Department of Biology, University of British Columbia Okanagan, Kelowna,

British Columbia, Canada. (2)Department of Paediatrics, Division of

Gastroenterology, Vancouver, British Columbia, Canada. (3)Departments of Medicine

& Dermatology and Skin Science, Child and Family Research Institute and

University of British Columbia, Vancouver, British Columbia, Canada.

 

Accumulating evidence supports that the intestinal microbiome is involved in Type

1 diabetes (T1D) pathogenesis through the gut-pancreas nexus. Our aim was to

determine whether the intestinal microbiota in the non-obese diabetic (NOD) mouse

model played a role in T1D through the gut. To examine the effect of the

intestinal microbiota on T1D onset, we manipulated gut microbes by: (1) the fecal

transplantation between non-obese diabetic (NOD) and resistant (NOR) mice and (2)

the oral antibiotic and probiotic treatment of NOD mice. We monitored diabetes

onset, quantified CD4+T cells in the Peyer's patches, profiled the microbiome and

measured fecal short-chain fatty acids (SCFA). The gut microbiota from NOD mice

harbored more pathobionts and fewer beneficial microbes in comparison with NOR

mice. Fecal transplantation of NOD microbes induced insulitis in NOR hosts

suggesting that the NOD microbiome is diabetogenic. Moreover, antibiotic exposure

accelerated diabetes onset in NOD mice accompanied by increased T-helper type 1

(Th1) and reduced Th17 cells in the intestinal lymphoid tissues. The diabetogenic

microbiome was characterized by a metagenome altered in several metabolic gene

clusters. Furthermore, diabetes susceptibility correlated with reduced fecal

SCFAs. In an attempt to correct the diabetogenic microbiome, we administered

VLS#3 probiotics to NOD mice but found that VSL#3 colonized the intestine poorly

and did not delay diabetes. We conclude that NOD mice harbor gut microbes that

induce diabetes and that their diabetogenic microbiome can be amplified early in

life through antibiotic exposure. Protective microbes like VSL#3 are insufficient

to overcome the effects of a diabetogenic microbiome.

 

DOI: 10.1038/ismej.2015.114

PMCID: PMC4737925 [Available on 2017-02-01]

PMID: 26274050  [PubMed - in process]

 

 

173. Psychoneuroendocrinology. 2016 Jan;63:217-27. doi:

10.1016/j.psyneuen.2015.10.001. Epub 2015 Oct 9.

 

Structural & functional consequences of chronic psychosocial stress on the

microbiome & host.

 

Bharwani A(1), Mian MF(2), Foster JA(3), Surette MG(4), Bienenstock J(1),

Forsythe P(5).

 

Author information:

(1)Department of Pathology & Molecular Medicine, McMaster University, 1280 Main

Street West Hamilton, Ontario L8S 4L8, Canada; McMaster Brain-Body Institute, St.

Joseph's Healthcare, 50 Charlton Avenue East Hamilton, Ontario L8N 4A6, Canada.

(2)McMaster Brain-Body Institute, St. Joseph's Healthcare, 50 Charlton Avenue

East Hamilton, Ontario L8N 4A6, Canada. (3)Department of Psychiatry & Behavioral

Neurosciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S

4L8, Canada; McMaster Brain-Body Institute, St. Joseph's Healthcare, 50 Charlton

Avenue East Hamilton, Ontario L8N 4A6, Canada. (4)Department of Medicine,

McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada;

Farncombe Family Digestive Health Research Institute, 1280 Main Street West,

Hamilton, Ontario L8S 4L8, Canada. (5)Department of Medicine, McMaster

University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada; Firestone

Institute for Respiratory Health, St. Joseph's Healthcare, 50 Charlton Avenue

East Hamilton, Ontario L8N 4A6, Canada; McMaster Brain-Body Institute, St.

Joseph's Healthcare, 50 Charlton Avenue East Hamilton, Ontario L8N 4A6, Canada.

Electronic address: forsytp@mcmaster.ca.

 

INTRODUCTION: Given the lasting impact of psychological distress on behavior,

along with the role of the microbiome in neurobehavioral development, we sought

to examine the relationship between the microbiota and stress-induced behavioral

deficits.

METHODS: Male C57BL/6 mice exposed to chronic social defeat were subjected to

behavioral analysis and profiling of the intestinal microbiome. Mice were also

analyzed for phenotypic and functional immune changes. A computational approach

on 16S rRNA marker gene sequences was used to predict functional changes in the

metagenome as a consequence of structural shifts in the microbiota.

RESULTS: Chronic social defeat induced behavioral changes that were associated

with reduced richness and diversity of the gut microbial community, along with

distinct shifts at the level of operational taxonomic units (OTU) across phyla.

The degree of deficits in social, but not exploratory behavior was correlated

with group differences between the microbial community profile. In silico

analysis predicted a shift in the functional profile of the microbiome: defeated

mice exhibited reduced functional diversity and a lower prevalence of pathways

involved in the synthesis and metabolism of neurotransmitter precursors and

short-chain fatty acids. Defeated mice also exhibited sustained alterations in

dendritic cell activation, and transiently elevated levels of IL-10+ T regulatory

cells that were suppressed over time.

CONCLUSIONS: This study indicates that stress-induced disruptions in neurologic

function are associated with altered immunoregulatory responses and complex

OTU-level shifts in the microbiota. It is thus suggested that a dysbiotic state,

along with specific changes in microbial markers, may predict the onset of

adverse neurocognitive deficits commonly observed following exposure to severe

stressors. The data also predict novel pathways that might underlie

microbiota-mediated effects on brain and behavior, thus presenting targets for

investigations into mechanisms and potential therapy.

 

Copyright © 2015 Elsevier Ltd. All rights reserved.

 

DOI: 10.1016/j.psyneuen.2015.10.001

PMID: 26479188  [PubMed - in process]

 

 

174. Diabetologia. 2014 Aug;57(8):1569-77. doi: 10.1007/s00125-014-3274-0. Epub 2014

Jun 15.

 

Aberrant gut microbiota composition at the onset of type 1 diabetes in young

children.

 

de Goffau MC(1), Fuentes S, van den Bogert B, Honkanen H, de Vos WM, Welling GW,

Hyöty H, Harmsen HJ.

 

Author information:

(1)Department of Medical Microbiology, University Medical Center Groningen,

University of Groningen, Hanzeplein 1, HPC EB80, 9713 GZ, Groningen, The

Netherlands.

 

AIMS/HYPOTHESIS: Recent studies indicate that an aberrant gut microbiota is

associated with the development of type 1 diabetes, yet little is known about the

microbiota in children who have diabetes at an early age. To this end, the

microbiota of children aged 1-5 years with new-onset type 1 diabetes was compared

with the microbiota of age-matched healthy controls.

METHODS: A deep global analysis of the gut microbiota composition was established

by phylogenetic microarray analysis using a Human Intestinal Tract Chip

(HITChip).

RESULTS: Principal component analyses highlighted the importance of age when

comparing age-matched pairs. In pairs younger than 2.9 years, the combined

abundance of the class Bacilli (notably streptococci) and the phylum

Bacteroidetes was higher in diabetic children, whereas the combined abundance of

members of Clostridium clusters IV and XIVa was higher in the healthy controls.

Controls older than 2.9 years were characterised by a higher fraction of

butyrate-producing species within Clostridium clusters IV and XIVa than was seen

in the corresponding diabetic children or in children from the younger age

groups, while the diabetic children older than 2.9 years could be differentiated

by having an increased microbial diversity.

CONCLUSIONS/INTERPRETATION: The results from both age groups suggest that

non-diabetic children have a more balanced microbiota in which butyrate-producing

species appear to hold a pivotal position.

 

DOI: 10.1007/s00125-014-3274-0

PMID: 24930037  [PubMed - indexed for MEDLINE]

 

 

175. Semin Reprod Med. 2014 Jan;32(1):5-13. doi: 10.1055/s-0033-1361817. Epub 2014 Jan

3.

 

Use of whole genome shotgun metagenomics: a practical guide for the

microbiome-minded physician scientist.

 

Ma J(1), Prince A(1), Aagaard KM(1).

 

Author information:

(1)Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology,

Baylor College of Medicine.

 

Whole genome shotgun sequencing (WGS) has been increasingly recognized as the

most comprehensive and robust approach for metagenomics research. When compared

with 16S-based metagenomics, it offers the advantage of identification of species

level taxonomy and the estimation of metabolic pathway activities from human and

environmental samples. Several large-scale metagenomic projects have been

recently conducted or are currently underway utilizing WGS. With the generation

of vast amounts of data, the bioinformatics and computational analysis of WGS

results become vital for the success of a metagenomics study. However, each step

in the WGS data analysis, including metagenome assembly, gene prediction,

taxonomy identification, function annotation, and pathway analysis, is

complicated by the shear amount of data. Algorithms and tools have been developed

specifically to handle WGS-generated metagenomics data with the hope of reducing

the requirement on computational time and storage space. Here, we present an

overview of the current state of metagenomics through WGS sequencing, challenges

frequently encountered, and up-to-date solutions. Several applications that are

uniquely applicable to microbiome studies in reproductive and perinatal medicine

are also discussed.

 

Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

 

DOI: 10.1055/s-0033-1361817

PMID: 24390915  [PubMed - indexed for MEDLINE]

 

 

176. PLoS One. 2015 Jun 15;10(6):e0129055. doi: 10.1371/journal.pone.0129055.

eCollection 2015.

 

Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is

Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort.

 

Gall A(1), Fero J(2), McCoy C(3), Claywell BC(3), Sanchez CA(2), Blount PL(4), Li

X(5), Vaughan TL(6), Matsen FA(3), Reid BJ(7), Salama NR(8).

 

Author information:

(1)Molecular and Cellular Biology Graduate Program, University of Washington,

Seattle, Washington, United States of America; Human Biology, Fred Hutchinson

Cancer Research Center, Seattle, Washington, United States of America. (2)Human

Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United

States of America. (3)Divisions of Public Health Sciences, Fred Hutchinson Cancer

Research Center, Seattle, Washington, United States of America; Program in

Computational Biology, Fred Hutchinson Cancer Research Center, Seattle,

Washington, United States of America. (4)Divisions of Public Health Sciences,

Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of

America; Department of Medicine, University of Washington School of Medicine,

Seattle, Washington, United States of America. (5)Human Biology, Fred Hutchinson

Cancer Research Center, Seattle, Washington, United States of America; Divisions

of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle,

Washington, United States of America. (6)Divisions of Public Health Sciences,

Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of

America; Department of Epidemiology, University of Washington, Seattle,

Washington, United States of America. (7)Human Biology, Fred Hutchinson Cancer

Research Center, Seattle, Washington, United States of America; Divisions of

Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle,

Washington, United States of America; Department of Medicine, University of

Washington School of Medicine, Seattle, Washington, United States of America;

Department of Genome Sciences, University of Washington, Seattle, Washington,

United States of America. (8)Human Biology, Fred Hutchinson Cancer Research

Center, Seattle, Washington, United States of America; Department of

Microbiology, University of Washington School of Medicine, Seattle, Washington,

United States of America.

 

BACKGROUND: The incidence of esophageal adenocarcinoma (EAC) has increased nearly

five-fold over the last four decades in the United States. Barrett's esophagus,

the replacement of the normal squamous epithelial lining with a mucus-secreting

columnar epithelium, is the only known precursor to EAC. Like other parts of the

gastrointestinal (GI) tract, the esophagus hosts a variety of bacteria and

comparisons among published studies suggest bacterial communities in the stomach

and esophagus differ. Chronic infection with Helicobacter pylori in the stomach

has been inversely associated with development of EAC, but the mechanisms

underlying this association remain unclear.

METHODOLOGY: The bacterial composition in the upper GI tract was characterized in

a subset of participants (n=12) of the Seattle Barrett's Esophagus Research

cohort using broad-range 16S PCR and pyrosequencing of biopsy and brush samples

collected from squamous esophagus, Barrett's esophagus, stomach corpus and

stomach antrum. Three of the individuals were sampled at two separate time

points. Prevalence of H. pylori infection and subsequent development of

aneuploidy (n=339) and EAC (n=433) was examined in a larger subset of this

cohort.

RESULTS/SIGNIFICANCE: Within individuals, bacterial communities of the stomach

and esophagus showed overlapping community membership. Despite closer proximity,

the stomach antrum and corpus communities were less similar than the antrum and

esophageal samples. Re-sampling of study participants revealed similar upper GI

community membership in two of three cases. In this Barrett's esophagus cohort,

Streptococcus and Prevotella species dominate the upper GI and the ratio of these

two species is associated with waist-to-hip ratio and hiatal hernia length, two

known EAC risk factors in Barrett's esophagus. H. pylori-positive individuals had

a significantly decreased incidence of aneuploidy and a non-significant trend

toward lower incidence of EAC.

 

DOI: 10.1371/journal.pone.0129055

PMCID: PMC4468150

PMID: 26076489  [PubMed - indexed for MEDLINE]

 

 

177. 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]

 

 

178. Microb Biotechnol. 2015 Jan;8(1):5-7.

 

Beyond borders: investigating microbiome interactivity and diversity for advanced

biocontrol technologies.

 

Berg G.

 

DOI: 10.1111/1751-7915.12235

PMCID: PMC4321355

PMID: 25627938  [PubMed - indexed for MEDLINE]

 

 

179. Helicobacter. 2016 Mar 18. doi: 10.1111/hel.12306. [Epub ahead of print]

 

Changes in the Functional Potential of the Gut Microbiome Following Probiotic

Supplementation during Helicobacter Pylori Treatment.

 

Oh B(1), Kim JW(2), Kim BS(3).

 

Author information:

(1)Department of Family Medicine, Seoul National University Boramae Hospital, 20

Boramae-ro 5-gil, Dongjak-gu, Seoul, 07061, Republic of Korea. (2)Department of

internal Medicine, Seoul National University Boramae Hospital, 20 Boramae-ro

5-gil, Dongjak-gu, Seoul, 07061, Republic of Korea. (3)Department of Life

Science, Hallym University, Chuncheon, Gangwon-do, 200-702, Republic of Korea.

 

BACKGROUND: Probiotic supplementation is utilized to alleviate the side effects

associated with antibiotic therapy for Helicobacter pylori infection. Several

studies have described the effects of administration of probiotics on the gut

microbiota during antibiotic therapy. However, most of these studies have focused

on specific bacteria, thereby providing limited information on the functional

roles of the altered microbiota. Therefore, we examined the impact of probiotic

supplementation on the structure and functional dynamics of the gut microbiota

during H. pylori eradication, using whole-metagenomic sequence analysis.

METHODS: Subjects were divided into two groups: the antibiotics group, which

received only antibiotics, and the probiotics group, which received antibiotics

with probiotic supplementation. The structural and functional profiles of gut

microbiota was analyzed using metagenomic DNA extracted from the feces during

treatment by Illumina MiSeq system.

RESULTS: The overall alterations in microbiota, as revealed by whole metagenome

sequencing, were similar with results from our previous 16S rRNA gene-based

analysis. The proportional shift in functional gene families was greater in the

antibiotics group than in the probiotics group. In particular, the proportion of

genes related to selenocompound metabolism was reduced in the probiotics group,

whereas genes associated with the metabolism of nucleotide sugars were increased.

CONCLUSION: The functional alterations of gut microbiota may link to the

reduction in intestinal irritation and maintenance of bacterial diversity

observed following probiotic supplementation with antibiotic therapy. The

potential beneficial roles of altered gut microbiota following probiotic

supplementation are expected a reduction in side effects such as intestinal

irritation and antibiotics resistance.

 

© 2016 John Wiley & Sons Ltd.

 

DOI: 10.1111/hel.12306

PMID: 26991862  [PubMed - as supplied by publisher]

 

 

180. PLoS One. 2015 Sep 10;10(9):e0137784. doi: 10.1371/journal.pone.0137784.

eCollection 2015.

 

A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with

Obesity.

 

Angelakis E(1), Armougom F(1), Carrière F(2), Bachar D(1), Laugier R(3), Lagier

JC(1), Robert C(1), Michelle C(1), Henrissat B(4), Raoult D(1).

 

Author information:

(1)URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine,

27 Bd Jean Moulin, 13385, Marseille, France. (2)CNRS, Aix Marseille Université,

UMR7282 Enzymology at Interfaces and Physiology of Lipolysis, 13009, Marseille,

France. (3)Hepato-gastroenterology Department, Hôpital de la Timone, Marseille,

France. (4)Architecture et Fonction des Macromolécules Biologiques, Centre

National de la Recherche Scientifique, Aix-Marseille Université, 13288,

Marseille, France; Department of Biological Sciences, King Abdulaziz University,

Jeddah, Saudi Arabia.

 

BACKGROUND: Few studies have tested the small intestine microbiota in humans,

where most nutrient digestion and absorption occur. Here, our objective was to

examine the duodenal microbiota between obese and normal volunteers using

metagenomic techniques.

METHODOLOGY/PRINCIPAL FINDINGS: We tested duodenal samples from five obese and

five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep

sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and

Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a

significant increase in anaerobic genera (p < 0.001) and a higher abundance of

genes encoding Acyl-CoA dehydrogenase (p = 0.0018) compared to the control group.

Obese individuals also had a reduced abundance of genes encoding sucrose

phosphorylase (p = 0.015) and 1,4-alpha-glucan branching enzyme (p = 0.05).

Normal weight people had significantly increased FabK (p = 0.027), and the

glycerophospholipid metabolism pathway revealed the presence of phospholipase A1

only in the control group (p = 0.05).

CONCLUSIONS/SIGNIFICANCE: The duodenal microbiota of obese individuals exhibit

alterations in the fatty acid and sucrose breakdown pathways, probably induced by

diet imbalance.

 

DOI: 10.1371/journal.pone.0137784

PMCID: PMC4565581

PMID: 26356733  [PubMed - indexed for MEDLINE]

 

 

 

Gigascience. 2016 Aug 2;5(1):34. doi: 10.1186/s13742-016-0140-7.

INC-Seq: accurate single molecule reads using nanopore sequencing.

Li C1,2, Chng KR1, Boey EJ1, Ng AH1, Wilm A1, Nagarajan N3,4.

Author information

Abstract

BACKGROUND:

Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read error rates (>10 %), including RNA-seq, haplotype sequencing and 16S sequencing.

RESULTS:

We developed the Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) as a strategy for obtaining long and accurate nanopore reads, starting with low input DNA. Applying INC-Seq for 16S rRNA-based bacterial profiling generated full-length amplicon sequences with a median accuracy >97 %.

CONCLUSIONS:

INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.

KEYWORDS:

Barcode sequencing; Consensus algorithms; Nanopore sequencing; Rolling circle amplification

PMID: 27485345 PMCID: PMC4970289 DOI: 10.1186/s13742-016-0140-7

[PubMed - in process] Free PMC Article

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42.

ISME J. 2016 Aug 2. doi: 10.1038/ismej.2016.108. [Epub ahead of print]

Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere.

Yan Y1,2, Kuramae EE1, de Hollander M1, Klinkhamer PG2, van Veen JA1,2.

Author information

Abstract

We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted suspensions of the same soil. We used 16S ribosomal RNA amplicon sequencing to determine the taxonomical structure of the bacterial communities and a shotgun metagenomics approach to investigate the potential functional diversity of the communities. By comparing the bacterial communities in soil and rhizosphere, the selective power of the plant was observed both at the taxonomic and functional level, although the diversity indices of soil and rhizosphere samples showed a highly variable, irregular pattern. Lesser variation, that is, more homogenization, was found for both the taxonomic structure and the functional profile of the rhizosphere communities as compared to the communities of the bulk soil. Network analysis revealed stronger interactions among bacterial operational taxonomic units in the rhizosphere than in the soil. The enrichment processes in the rhizosphere selected microbes with particular functional genes related to transporters, the Embden-Meyerhof-Parnas pathway and hydrogen metabolism. This selection was not random across bacteria with these functional traits, but it was species specific. Overall, this suggests that functional traits are a key to the assembly of bacterial rhizosphere communities.The ISME Journal advance online publication, 2 August 2016; doi:10.1038/ismej.2016.108.

PMID: 27482928 DOI: 10.1038/ismej.2016.108

[PubMed - as supplied by publisher]

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43.

ISME J. 2016 Aug 2. doi: 10.1038/ismej.2016.98. [Epub ahead of print]

Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner.

Klümper U1, Dechesne A1, Riber L2, Brandt KK3, Gülay A1, Sørensen SJ2, Smets BF1.

Author information

Abstract

The environmental stimulants and inhibitors of conjugal plasmid transfer in microbial communities are poorly understood. Specifically, it is not known whether exposure to stressors may cause a community to alter its plasmid uptake ability. We assessed whether metals (Cu, Cd, Ni, Zn) and one metalloid (As), at concentrations causing partial growth inhibition, modulate community permissiveness (that is, uptake ability) against a broad-host-range IncP-type plasmid (pKJK5). Cells were extracted from an agricultural soil as recipient community and a cultivation-minimal filter mating assay was conducted with an exogenous E. coli donor strain. The donor hosted a gfp-tagged pKJK5 derivative from which conjugation events could be microscopically quantified and transconjugants isolated and phylogenetically described at high resolution via FACS and 16S rRNA amplicon sequencing. Metal stress consistently decreased plasmid transfer frequencies to the community, while the transconjugal pool richness remained unaffected with OTUs belonging to 12 bacterial phyla. The taxonomic composition of the transconjugal pools was distinct from their respective recipient communities and clustered dependent on the stress type and dose. However, for certain OTUs, stress increased or decreased permissiveness by more than 1000-fold and this response was typically correlated across different metals and doses. The response to some stresses was, in addition, phylogenetically conserved. This is the first demonstration that community permissiveness is sensitive to metal(loid) stress in a manner that is both partially consistent across stressors and phylogenetically conserved.The ISME Journal advance online publication, 2 August 2016; doi:10.1038/ismej.2016.98.

PMID: 27482924 DOI: 10.1038/ismej.2016.98

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44.

Environ Sci Technol. 2016 Sep 6;50(17):9279-88. doi: 10.1021/acs.est.6b02007. Epub 2016 Aug 18.

Biofilm Thickness Influences Biodiversity in Nitrifying MBBRs-Implications on Micropollutant Removal.

Torresi E1,2, Fowler SJ1, Polesel F1, Bester K3, Andersen HR1, Smets BF1, Plósz BG1, Christensson M2.

Author information

Abstract

In biofilm systems for wastewater treatment (e.g., moving bed biofilms reactors-MBBRs) biofilm thickness is typically not under direct control. Nevertheless, biofilm thickness is likely to have a profound effect on the microbial diversity and activity, as a result of diffusion limitation and thus substrate penetration in the biofilm. In this study, we investigated the impact of biofilm thickness on nitrification and on the removal of more than 20 organic micropollutants in laboratory-scale nitrifying MBBRs. We used novel carriers (Z-carriers, AnoxKaldnes) that allowed controlling biofilm thickness at 50, 200, 300, 400, and 500 μm. The impact of biofilm thickness on microbial community was assessed via 16S rRNA gene amplicon sequencing and ammonia monooxygenase (amoA) abundance quantification through quantitative PCR (qPCR). Results from batch experiments and microbial analysis showed that (i) the thickest biofilm (500 μm) presented the highest specific biotransformation rate constants (kbio, L g(-1) d(-1)) for 14 out of 22 micropollutants; (ii) biofilm thickness positively associated with biodiversity, which was suggested as the main factor for the observed enhancement of kbio; (iii) the thinnest biofilm (50 μm) exhibited the highest nitrification rate (gN d(-1) g(-1)), amoA gene abundance and kbio values for some of the most recalcitrant micropollutants (i.e., diclofenac and targeted sulfonamides). Although thin biofilms favored nitrification activity and the removal of some micropollutants, treatment systems based on thicker biofilms should be considered to enhance the elimination of a broad spectrum of micropollutants.

PMID: 27477857 DOI: 10.1021/acs.est.6b02007

[PubMed - in process]

 

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