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16s rRNA Sequencing with MR DNA

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

 

 

21. J Microbiol Methods. 2015 Dec;119:239-42. doi: 10.1016/j.mimet.2015.11.001. Epub

2015 Nov 10.

 

Changes in 16s RNA Gene Microbial Community Profiling by Concentration of

Prokaryotic DNA.

 

Glassing A(1), Dowd SE(2), Galandiuk S(3), Davis B(4), Jorden JR(3), Chiodini

RJ(5).

 

Author information:

(1)Department of Biological and Physical Sciences, Montana State

University-Billings, Billings, Montana, United States. (2)Molecular Research (Mr.

DNA), Shallowater, Texas, United States. (3)Department of Surgery, University of

Louisville, Louisville, Kentucky, United States. (4)Department of Surgery, Paul

L. Foster School of Medicine, Texas Tech University Health Sciences Center, El

Paso, Texas, United States. (5)St. Vincent Healthcare, Sisters of Charity of

Leavenworth Health System, Billings, Montana, United States; Department of

Biological and Physical Sciences, Montana State University-Billings, Billings,

Montana, United States. Electronic address: rodrick.chiodini@msubillings.edu.

 

Microbial metagenomics are hindered in clinical tissue samples as a result of the

large relative amount of human DNA in relation to microbial DNA acting as

competitive inhibitors of downstream applications. We evaluated the LOOXSTER®

Enrichment Kit to separate eukaryotic and prokaryotic DNA in submucosal

intestinal tissue samples having a low microbial biomass and to determine the

effects of enrichment on 16s rRNA microbiota sequencing. The enrichment kit

reduced the amount of human DNA in the samples 40-70% resulting in a 3.5-fold

increase in the number of 16s bacterial gene sequences detected on the Illumina

MiSeq platform. This increase was accompanied by the detection of 41 additional

bacterial genera and 94 tentative species. The additional bacterial taxa detected

accounted for as much as 25% of the total bacterial population that significantly

altered the relative prevalence and composition of the intestinal microbiota. The

ability to reduce the competitive inhibition created by human DNA and the

concentration of bacterial DNA may allow metagenomics to be performed on complex

tissues containing a low bacterial biomass.

 

Copyright © 2015 Elsevier B.V. All rights reserved.

 

DOI: 10.1016/j.mimet.2015.11.001

PMID: 26569458  [PubMed - indexed for MEDLINE]

 

 

22. Microbiome. 2014 Jul 11;2:24. doi: 10.1186/2049-2618-2-24. eCollection 2014.

 

Effect of chemotherapy on the microbiota and metabolome of human milk, a case

report.

 

Urbaniak C(1), McMillan A(1), Angelini M(2), Gloor GB(3), Sumarah M(4), Burton

JP(1), Reid G(1).

 

Author information:

(1)Lawson Health Research Institute, 268 Grosvenor Street, London, ON N6A 4V2,

Canada ; Department of Microbiology & Immunology, Western University, London, ON

N6A 5C1, Canada. (2)Perinatal and Women's Health, London Health Sciences Centre,

London, ON N6A 4L6, Canada. (3)Department of Biochemistry, Western University,

London, ON N6A 5C1, Canada. (4)Department of Chemistry, Western University,

London, ON N6A 5C1, Canada ; Agriculture and Agri-Food Canada, London, ON N5V

4T3, Canada.

 

BACKGROUND: Human milk is an important source of bacteria for the developing

infant and has been shown to influence the bacterial composition of the neonatal

gut, which in turn can affect disease risk later in life. Human milk is also an

important source of nutrients, influencing bacterial composition but also

directly affecting the host. While recent studies have emphasized the adverse

effects of antibiotic therapy on the infant microbiota, the effects of maternal

chemotherapy have not been previously studied. Here we report the effects of drug

administration on the microbiota and metabolome of human milk.

METHODS: Mature milk was collected every two weeks over a four month period from

a lactating woman undergoing chemotherapy for Hodgkin's lymphoma. Mature milk was

also collected from healthy lactating women for comparison. Microbial profiles

were analyzed by 16S sequencing and the metabolome by gas chromatography-mass

spectrometry.

FINDINGS: Chemotherapy caused a significant deviation from a healthy microbial

and metabolomic profile, with depletion of genera Bifidobacterium, Eubacterium,

Staphylococcus and Cloacibacterium in favor of Acinetobacter, Xanthomonadaceae

and Stenotrophomonas. The metabolites docosahexaenoic acid and inositol known for

their beneficial effects were also decreased.

CONCLUSION: With milk contents being critical for shaping infant immunity and

development, consideration needs to be given to the impact of drugs administered

to the mother and the long-term potential consequences for the health of the

infant.

 

DOI: 10.1186/2049-2618-2-24

PMCID: PMC4109383

PMID: 25061513  [PubMed]

 

 

23. Hepatology. 2016 Sep 17. doi: 10.1002/hep.28829. [Epub ahead of print]

 

Changes in blood microbiota profiles associated with liver fibrosis in obese

patients: A pilot analysis.

 

Lelouvier B(1), Servant F(2), Païssé S(2), Brunet AC(2,)(3), Benyahya S(2),

Serino M(4), Valle C(2), Rosa Ortiz M(5), Puig J(6), Courtney M(2), Federici

M(7), Manuel Fernández-Real J(5), Burcelin R(2,)(4), Amar J(8,)(9,)(10).

 

Author information:

(1)Vaiomer SAS, Labège, France. benjamin.lelouvier@vaiomer.com. (2)Vaiomer SAS,

Labège, France. (3)IMT, Université Paul Sabatier, Toulouse, France. (4)INSERM

U1048, I2MC, Toulouse, France. (5)Department of Diabetes, Endocrinology, and

Nutrition, IDIBGI, Girona, Spain. (6)Department of Radiology, IDI, IDIBGI,

Girona, Spain. (7)Department of Systems Medicine and Center for Atherosclerosis,

University of Rome "Tor Vergata", Rome, Italy. (8)Vaiomer SAS, Labège, France.

amar.j@chu-toulouse.fr. (9)INSERM U1048, I2MC, Toulouse, France.

amar.j@chu-toulouse.fr. (10)Department of Therapeutics, Rangueil Hospital,

Toulouse, France. amar.j@chu-toulouse.fr.

 

OBJECTIVE: The early detection of liver fibrosis among patients with nonalcoholic

fatty liver disease (NAFLD) is an important clinical need. In view of the

suggested role played by bacterial translocation in liver disease and obesity, we

sought to investigate the relationship between blood microbiota and liver

fibrosis in European cohorts of patients with severe obesity.

DESIGN: We carried out a cross-sectional study of obese patients,

well-characterized with respect to the severity of the NAFLD, in the cohort

FLORINASH. This cohort has been divided into a discovery cohort comprising 50

Spanish patients and then in a validation cohort of 71 Italian patients. Blood

bacterial DNA was analyzed both quantitatively by 16S rDNA qPCR and qualitatively

by 16S rDNA targeted metagenomic sequencing and functional metagenome prediction.

Spanish plasma bile acid contents were analyzed by LC/MS.

RESULTS: The 16S rDNA concentration was significantly higher in patients of the

discovery cohort with liver fibrosis. By 16S sequencing, we found specific

differences in the proportion of several bacterial taxa in both blood and feces

that correlate with the presence of liver fibrosis thus defining a specific

signature of the liver disease. Several secondary/primary bile acids ratios were

also decreased with liver fibrosis in the discovery cohort. We confirmed in the

validation cohort the correlation between blood 16S rDNA concentration and liver

fibrosis whereas we did not confirm the specific bacterial taxa signature,

despite a similar trend in patients with more severe fibrosis.

CONCLUSIONS: We have shown that changes in blood microbiota are associated with

liver fibrosis in obese patients. Blood microbiota analysis provides potential

biomarkers for the detection of liver fibrosis in this population. This article

is protected by copyright. All rights reserved.

 

© 2016 by the American Association for the Study of Liver Diseases.

 

DOI: 10.1002/hep.28829

PMID: 27639192  [PubMed - as supplied by publisher]

 

81. Microbiome. 2015 Nov 26;3:56. doi: 10.1186/s40168-015-0118-1.

 

Metagenomic analysis of the microbiota in the highly compartmented hindguts of

six wood- or soil-feeding higher termites.

 

Rossmassler K(1,)(2), Dietrich C(1), Thompson C(1), Mikaelyan A(1,)(3), Nonoh

JO(1), Scheffrahn RH(4), Sillam-Dussès D(5,)(6), Brune A(7,)(8).

 

Author information:

(1)Department of Biogeochemistry, Max Planck Institute for Terrestrial

Microbiology, Marburg, Germany. (2)Present address: Department of Civil and

Environmental Engineering, Colorado State University, Fort Collins, CO, USA.

(3)LOEWE Center for Synthetic Microbiology (Synmikro), Philipps-Universität

Marburg, Marburg, Germany. (4)Fort Lauderdale Research and Education Center,

University of Florida, Davie, FL, USA. (5)Laboratory of Experimental and

Comparative Ethology, University Paris 13, EA4443, Sorbonne Paris Cité,

Villetaneuse, France. (6)Institute of Research for Development-Sorbonne

Universités, Institute of Ecology and Environmental Sciences, U242, Bondy,

France. (7)Department of Biogeochemistry, Max Planck Institute for Terrestrial

Microbiology, Marburg, Germany. brune@mpi-marburg.mpg.de. (8)LOEWE Center for

Synthetic Microbiology (Synmikro), Philipps-Universität Marburg, Marburg,

Germany. brune@mpi-marburg.mpg.de.

 

BACKGROUND: Termites are important contributors to carbon and nitrogen cycling in

tropical ecosystems. Higher termites digest lignocellulose in various stages of

humification with the help of an entirely prokaryotic microbiota housed in their

compartmented intestinal tract. Previous studies revealed fundamental differences

in community structure between compartments, but the functional roles of

individual lineages in symbiotic digestion are mostly unknown.

RESULTS: Here, we conducted a highly resolved analysis of the gut microbiota in

six species of higher termites that feed on plant material at different levels of

humification. Combining amplicon sequencing and metagenomics, we assessed

similarities in community structure and functional potential between the major

hindgut compartments (P1, P3, and P4). Cluster analysis of the relative

abundances of orthologous gene clusters (COGs) revealed high similarities among

wood- and litter-feeding termites and strong differences to humivorous species.

However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly

differed from those based on protein-coding genes.

CONCLUSION: Community structure and functional potential of the microbiota in

individual gut compartments are clearly driven by the digestive strategy of the

host. The metagenomics libraries obtained in this study provide the basis for

future studies that elucidate the fundamental differences in the

symbiont-mediated breakdown of lignocellulose and humus by termites of different

feeding groups. The high proportion of uncultured bacterial lineages in all

samples calls for a reference-independent approach for the correct taxonomic

assignment of protein-coding genes.

 

DOI: 10.1186/s40168-015-0118-1

PMCID: PMC4660790

PMID: 26607965  [PubMed - indexed for MEDLINE]

 

 

82. Appl Environ Microbiol. 2013 Oct;79(20):6196-206. doi: 10.1128/AEM.01641-13. Epub

2013 Aug 2.

 

Metagenome survey of a multispecies and alga-associated biofilm revealed key

elements of bacterial-algal interactions in photobioreactors.

 

Krohn-Molt I(1), Wemheuer B, Alawi M, Poehlein A, Güllert S, Schmeisser C,

Pommerening-Röser A, Grundhoff A, Daniel R, Hanelt D, Streit WR.

 

Author information:

(1)University of Hamburg, Biocenter Klein Flottbek, Microbiology and

Biotechnology, Hamburg, Germany.

 

Photobioreactors (PBRs) are very attractive for sunlight-driven production of

biofuels and capturing of anthropogenic CO2. One major problem associated with

PBRs however, is that the bacteria usually associated with microalgae in

nonaxenic cultures can lead to biofouling and thereby affect algal productivity.

Here, we report on a phylogenetic, metagenome, and functional analysis of a

mixed-species bacterial biofilm associated with the microalgae Chlorella vulgaris

and Scenedesmus obliquus in a PBR. The biofilm diversity and population dynamics

were examined through 16S rRNA phylogeny. Overall, the diversity was rather

limited, with approximately 30 bacterial species associated with the algae. The

majority of the observed microorganisms were affiliated with Alphaproteobacteria,

Betaproteobacteria, and Bacteroidetes. A combined approach of sequencing via GS

FLX Titanium from Roche and HiSeq 2000 from Illumina resulted in the overall

production of 350 Mbp of sequenced DNA, 165 Mbp of which was assembled in larger

contigs with a maximum size of 0.2 Mbp. A KEGG pathway analysis suggested high

metabolic diversity with respect to the use of polymers and aromatic and

nonaromatic compounds. Genes associated with the biosynthesis of essential B

vitamins were highly redundant and functional. Moreover, a relatively high number

of predicted and functional lipase and esterase genes indicated that the

alga-associated bacteria are possibly a major sink for lipids and fatty acids

produced by the microalgae. This is the first metagenome study of microalga- and

PBR-associated biofilm bacteria, and it gives new clues for improved biofuel

production in PBRs.

 

DOI: 10.1128/AEM.01641-13

PMCID: PMC3811195

PMID: 23913425  [PubMed - indexed for MEDLINE]

 

 

83. Vet Microbiol. 2013 Mar 23;162(2-4):891-8. doi: 10.1016/j.vetmic.2012.11.018.

Epub 2012 Nov 20.

 

Metagenomic analysis of the canine oral cavity as revealed by high-throughput

pyrosequencing of the 16S rRNA gene.

 

Sturgeon A(1), Stull JW, Costa MC, Weese JS.

 

Author information:

(1)Department of Pathobiology, Ontario Veterinary College, University of Guelph,

Guelph, Ontario N1G 2W1, Canada. asturgeo@uoguelph.ca

 

Efficient characterization of the canine oral microbiome is critical for

understanding the role of oral bacteria in health and for providing insight into

early diagnosis and treatment strategies against periodontal disease. To date,

characterization has been limited to cloning-based sequencing and conventional

culture-based studies, which generally underestimate community diversity as a

result of inherent biases in their methodologies. Pyrosequencing, a cloning- and

culture-independent sequencing approach, eliminates these elements of bias from

the analysis and enables extensive sequencing of microbial populations. In this

report, pyrosequencing of the 16S rRNA gene was used to examine oral samples from

six healthy dogs in an effort to determine community membership, diversity, and

zoonotic implications. Pyrosequencing revealed a mean (SD) of 226 (59)

operational taxonomic units (OTUs, 97% similarity), representing 181 genera from

13 bacterial phyla. The phyla Bacteroidetes (60.2%), Proteobacteria (20.8%),

Firmicutes (11.4%), Fusobacteria (4.7%), and Spirochaetes (1.7%) predominated.

The most commonly identified genera were Porphyromonas (39.2% of sequences),

Fusobacterium (4.5%), Capnocytophaga (3.8%), Derxia (3.7%), Moraxella (3.3%), and

Bergeyella (2.7%). Fifty-six OTUs, corresponding to 38 unique genus-level

identifications, were present in all samples, which supports the concept of a

stable core microbiome existing between healthy dogs. Potentially zoonotic and

periodontal bacteria were detected in all dogs, and highlights the zoonotic and

disease potential of the oral microflora. Results suggest that the canine oral

cavity harbors a rich and diverse bacterial community, and exceeds estimates by

previous culture- and cloning-based studies.

 

Copyright © 2012 Elsevier B.V. All rights reserved.

 

DOI: 10.1016/j.vetmic.2012.11.018

PMID: 23228621  [PubMed - indexed for MEDLINE]

 

 

84. Antonie Van Leeuwenhoek. 2012 Feb;101(2):205-15. doi: 10.1007/s10482-011-9624-8.

Epub 2011 Jul 27.

 

Taxonomic and functional assignment of cloned sequences from high Andean forest

soil metagenome.

 

Montaña JS(1), Jiménez DJ, Hernández M, Angel T, Baena S.

 

Author information:

(1)Department of Microbiology, Pontificia Universidad Javeriana, Carrera 7 No.

43-82, Building 53, P.O. Box 5671, Bogotá, DC, Colombia.

jose.montana@javeriana.edu.co

 

Total metagenomic DNA was isolated from high Andean forest soil and subjected to

taxonomical and functional composition analyses by means of clone library

generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used

to construct a metagenomic library of approximately 20,000 clones (in the plasmid

p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the

total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were

sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs

(0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX,

resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the

metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer

v3.8 software, respectively. Most clone sequences were classified as Bacteria

belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the

most represented orders were Actinomycetales (34% average), Rhizobiales,

Burkholderiales and Myxococcales and with a greater number of sequences in the

genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The

vast majority of sequences were associated with the metabolism of carbohydrates,

proteins, lipids and catalytic functions, such as phosphatases,

glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and

epoxide hydrolases. In this study we compared different methods of taxonomic and

functional assignment of metagenomic clone sequences to evaluate microbial

diversity in an unexplored soil ecosystem, searching for putative enzymes of

biotechnological interest and generating important information for further

functional screening of clone libraries.

 

DOI: 10.1007/s10482-011-9624-8

PMID: 21792685  [PubMed - indexed for MEDLINE]

 

 

85. PLoS One. 2015 Apr 13;10(4):e0123990. doi: 10.1371/journal.pone.0123990.

eCollection 2015.

 

Bacterial community associated with the intestinal tract of Chinese mitten crab

(Eriocheir sinensis) farmed in Lake Tai, China.

 

Chen X(1), Di P(1), Wang H(1), Li B(2), Pan Y(3), Yan S(4), Wang Y(3).

 

Author information:

(1)Laboratory of Quality and Safety Risk Assessment for Aquatic Products on

Storage & Preservation, Ministry of Agriculture, Shanghai, China; College of Food

Science and Technology, Shanghai Ocean University, Shanghai, China. (2)College of

Food Science and Technology, Shanghai Ocean University, Shanghai, China.

(3)Laboratory of Quality and Safety Risk Assessment for Aquatic Products on

Storage & Preservation, Ministry of Agriculture, Shanghai, China; Shanghai

Engineering Research Center of Aquatic-Product Processing & Preservation,

Shanghai, China; College of Food Science and Technology, Shanghai Ocean

University, Shanghai, China. (4)Institute of Biochemistry and Molecular Cell

Biology, University of Goettingen, Goettingen, Germany.

 

Chinese mitten crab (CMC, Eriocheir sinensis) is an economically valuable species

in South-East Asia that has been widely farmed in China. Characterization of the

intestinal bacterial diversity of CMC will provide insights into the

aquaculturing of CMCs. Based on the analysis of cloned 16S rRNA genes from

culture-independent CMC gut bacteria, 124 out of 128 different clones reveal >95%

nucleotide similarity to the species belonging to the four phyla of Tenericutes,

Bacteroidetes, Firmicutes and Proteobacteria; one clone shows 91% sequence

similarity to the member of TM7 (a candidate phylum without cultured

representatives). Fluorescent in situ hybridization also reveals the abundance of

Bacteroidetes in crab intestine. Electron micrographs show that spherical and

filamentous bacteria are closely associated with the microvillus brush border of

the midgut epithelium and are often inserted into the space between the

microvilli using a stalk-like cell appendage. In contrast, the predominant

rod-shaped bacteria in the hindgut are tightly attached to the epithelium surface

by an unusual pili-like structure. Both 16S rRNA gene denaturing gel gradient

electrophoresis and metagenome library indicate that the CMC Mollicutes group 2

appears to be present in both the midgut and hindgut with no significant

difference in abundance. The CMC Mollicutes group 1, however, was found mostly in

the midgut of CMCs. The CMC gut Mollicutes phylotypes appear to be most closely

related to Mollicutes symbionts detected in the gut of isopods (Crustacea:

Isopoda). Overall, the results suggest that CMCs harbor diverse, novel and

specific gut bacteria, which are likely to live in close relationships with the

CMC host.

 

DOI: 10.1371/journal.pone.0123990

PMCID: PMC4395229

PMID: 25875449  [PubMed - indexed for MEDLINE]

 

 

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

2015 Sep 4.

 

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

Processing Environment.

 

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

 

Author information:

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

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

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

ercolini@unina.it.

 

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

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

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

amplicon sequencing. Environmental samples from surfaces and tools were studied

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

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

operational taxonomic units with extremely variable relative abundances (0.01 to

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

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

of Streptococcus thermophilus and possible spoilage-associated bacteria,

including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative

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

Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii.

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

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

predicted metagenomes also indicated differential distribution of metabolic

pathways between the two categories of samples. Cooccurrence and coexclusion

pattern analyses indicated that the occurrence of potential spoilers was excluded

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

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

cheeses, with possible negative effects on their microbiological quality.

 

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

 

DOI: 10.1128/AEM.02294-15

PMCID: PMC4616952

PMID: 26341209  [PubMed - indexed for MEDLINE]

 

 

87. Sci Rep. 2015 Apr 8;5:9456. doi: 10.1038/srep09456.

 

A pyrosequencing insight into sprawling bacterial diversity and community

dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies.

 

Hoppe B(1), Krger K(2), Kahl T(3), Arnstadt T(4), Buscot F(5), Bauhus J(3), Wubet

T(5).

 

Author information:

(1)1] Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental

Research, Halle (Saale), Germany [2] Chair of Silviculture, Faculty of

Environment and Natural Resources, University of Freiburg, Freiburg i. Brsg.,

Germany. (2)Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental

Research, Halle (Saale), Germany. (3)Chair of Silviculture, Faculty of

Environment and Natural Resources, University of Freiburg, Freiburg i. Brsg.,

Germany. (4)Department of Bio- and Environmental Sciences, TU Dresden,

International Institute Zittau, Zittau, Germany. (5)1] Department of Soil

Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle (Saale),

Germany [2] The German Centre for Integrative Biodiversity Research (iDiv),

University Leipzig, Leipzig, Germany.

 

Deadwood is an important biodiversity hotspot in forest ecosystems. While

saproxylic insects and wood-inhabiting fungi have been studied extensively,

little is known about deadwood-inhabiting bacteria. The study we present is among

the first to compare bacterial diversity and community structure of deadwood

under field conditions. We therefore compared deadwood logs of two temperate

forest tree species Fagus sylvatica and Picea abies using 16S rDNA pyrosequencing

to identify changes in bacterial diversity and community structure at different

stages of decay in forest plots under different management regimes.

Alphaproteobacteria, Acidobacteria and Actinobacteria were the dominant taxonomic

groups in both tree species. There were no differences in bacterial OTU richness

between deadwood of Fagus sylvatica and Picea abies. Bacteria from the order

Rhizobiales became more abundant during the intermediate and advanced stages of

decay, accounting for up to 25% of the entire bacterial community in such logs.

The most dominant OTU was taxonomically assigned to the genus Methylovirgula,

which was recently described in a woodblock experiment of Fagus sylvatica.

Besides tree species we were able to demonstrate that deadwood physico-chemical

properties, in particular remaining mass, relative wood moisture, pH, and C/N

ratio serve as drivers of community composition of deadwood-inhabiting bacteria.

 

DOI: 10.1038/srep09456

PMCID: PMC4389208

PMID: 25851097  [PubMed - indexed for MEDLINE]

 

 

88. World J Gastroenterol. 2015 Mar 7;21(9):2759-69. doi: 10.3748/wjg.v21.i9.2759.

 

Fecal microbes, short chain fatty acids, and colorectal cancer across

racial/ethnic groups.

 

Hester CM(1), Jala VR(1), Langille MG(1), Umar S(1), Greiner KA(1), Haribabu

B(1).

 

Author information:

(1)Christina M Hester, K Allen Greiner, Department of Family Medicine Research

Division, University of Kansas Medical Center, Kansas City, KS 66160, United

States.

 

AIM: To investigate differences in microbes and short chain fatty acid (SCFA)

levels in stool samples from Hispanic and non-Hispanic African American, American

Indian, and White participants.

METHODS: Stool samples from twenty participants were subjected to analysis for

relative levels of viable bacteria and for SCFA levels. Additionally, the samples

were subjected to 16S rRNA gene pyrosequencing for identification of bacteria

present in the stool. We used a metagenome functional prediction technique to

analyze genome copy numbers and estimate the abundance of butyrate kinase in all

samples.

RESULTS: We found that African Americans had significantly lower levels of

acetate, butyrate, and total SCFAs than all other racial/ethnic groups. We also

found that participant microbial profiles differed by racial/ethnic group.

African Americans had significantly more Firmicutes than Whites, with enriched

Ruminococcaceae. The Firmicutes/Bacteroidetes ratio was also significantly higher

for African Americans than for Whites (P = 0.049). We found Clostridium levels to

be significantly and inversely related to total SCFA levels (P = 0.019) and we

found Bacteroides to be positively associated (P = 0.027) and Clostridium to be

negatively associated (P = 0.012) with levels of butyrate. We also identified a

correlation between copy number for a butyrate kinase predicted from 16S rRNA

gene abundance and levels of butyrate in stool.

CONCLUSION: The identified differences in gut flora and SCFA levels may relate to

colorectal cancer mortality differentials and may be useful as targets for future

clinical and behavioral interventions.

 

DOI: 10.3748/wjg.v21.i9.2759

PMCID: PMC4351229

PMID: 25759547  [PubMed - indexed for MEDLINE]

 

 

89. J Infect Dis. 2013 Apr;207(7):1105-14. doi: 10.1093/infdis/jit005. Epub 2013 Jan

8.

 

Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic

men.

 

Redel H(1), Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G,

Sodergren E, Blaser MJ.

 

Author information:

(1)Department of Medicine, New York University School of Medicine, New York, NY

10010, USA. henry.redel@gmail.com

 

BACKGROUND: Diabetic foot infections are a leading cause of lower extremity

amputations. Our study examines the microbiota of diabetic skin prior to ulcer

development or infection.

METHODS: In a case-control study, outpatient males were recruited at a veterans

hospital. Subjects were swabbed at 4 cutaneous sites, 1 on the forearm and 3 on

the foot. Quantitative polymerase chain reaction (qPCR) with primers and probes

specific for bacteria, Staphylococcus species, Staphylococcus aureus, and fungi

were performed on all samples. High-throughput 16S ribosomal RNA (rRNA)

sequencing was performed on samples from the forearm and the plantar aspect of

the foot.

RESULTS: qPCR analysis of swab specimens from 30 diabetic subjects and 30 control

subjects showed no differences in total numbers of bacteria or fungi at any

sampled site. Increased log concentrations of Staphylococcus aureus, quantified

by the number of nuc gene copies, were present in diabetic men on the plantar

aspect of the foot. High-throughput 16S rRNA sequencing found that, on the foot,

the microbiota in controls (n = 24) was dominated by Staphylococcus species,

whereas the microbiota in diabetics (n = 23) was more diverse at the genus level.

The forearm microbiota had similar diversity in diabetic and control groups.

CONCLUSIONS: The feet of diabetic men had decreased populations of Staphylococcus

species, increased populations of S. aureus, and increased bacterial diversity,

compared with the feet of controls. These ecologic changes may affect the risk

for wound infections.

 

DOI: 10.1093/infdis/jit005

PMCID: PMC3583274

PMID: 23300163  [PubMed - indexed for MEDLINE]

 

 

90. BMC Genomics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2164-14-S5-S16. Epub 2013

Oct 16.

 

Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and

SOLiD shotgun sequencing.

 

Mitra S, Förster-Fromme K, Damms-Machado A, Scheurenbrand T, Biskup S, Huson DH,

Bischoff SC.

 

BACKGROUND: Metagenomics seeks to understand microbial communities and

assemblages by DNA sequencing. Technological advances in next generation

sequencing technologies are fuelling a rapid growth in the number and scope of

projects aiming to analyze complex microbial environments such as marine, soil or

the gut. Recent improvements in longer read lengths and paired-sequencing allow

better resolution in profiling microbial communities. While both 454 sequencing

and Illumina sequencing have been used in numerous metagenomic studies, SOLiD

sequencing is not commonly used in this area, as it is believed to be more

suitable in the context of reference-guided projects.

RESULTS: To investigate the performance of SOLiD sequencing in a metagenomic

context, we compared taxonomic profiles of SOLiD mate-pair sequencing reads with

Sanger paired reads and 454 single reads. All sequences were obtained from the

bacterial 16S rRNA gene, which was amplified from microbial DNA extracted from a

human fecal sample. Additionally, from the same fecal sample, complete genomic

microbial DNA was extracted and shotgun sequenced using SOLiD sequencing to study

the composition of the intestinal microbiota and the existing microbial

metabolism. We found that the microbiota composition of 16S rRNA gene sequences

obtained using Sanger, 454 and SOLiD sequencing provide results comparable to the

result based on shotgun sequencing. Moreover, with SOLiD sequences we obtained

more resolution down to the species level. In addition, the shotgun data allowed

us to determine a functional profile using the databases SEED and KEGG.

CONCLUSIONS: This study shows that SOLiD mate-pair sequencing is a viable and

cost-efficient option for analyzing a complex microbiome. To the best of our

knowledge, this is the first time that SOLiD sequencing has been used in a human

sample.

 

DOI: 10.1186/1471-2164-14-S5-S16

PMCID: PMC3852202

PMID: 24564472  [PubMed - indexed for MEDLINE]

 

 

91. Biofouling. 2014;30(10):1211-23. doi: 10.1080/08927014.2014.977267.

 

Integrated metagenomic and metaproteomic analyses of marine biofilm communities.

 

Leary DH(1), Li RW, Hamdan LJ, Hervey WJ 4th, Lebedev N, Wang Z, Deschamps JR,

Kusterbeck AW, Vora GJ.

 

Author information:

(1)a Center for Bio/Molecular Science and Engineering , US Naval Research

Laboratory , Washington , DC , USA.

 

Metagenomic and metaproteomic analyses were utilized to determine the composition

and function of complex air-water interface biofilms sampled from the hulls of

two US Navy destroyers. Prokaryotic community analyses using PhyloChip-based 16S

rDNA profiling revealed two significantly different and taxonomically rich

biofilm communities (6,942 taxa) in which the majority of unique taxa were

ascribed to members of the Gammaproteobacteria, Alphaproteobacteria and

Clostridia. Although metagenomic sequencing indicated that both biofilms were

dominated by prokaryotic sequence reads (> 91%) with the majority of the

bacterial reads belonging to the Alphaproteobacteria, the Ship-1 metagenome

harbored greater organismal and functional diversity and was comparatively

enriched for sequences from Cyanobacteria, Bacteroidetes and macroscopic

eukaryotes, whereas the Ship-2 metagenome was enriched for sequences from

Proteobacteria and microscopic photosynthetic eukaryotes. Qualitative liquid

chromatography-tandem mass spectrometry metaproteome analyses identified 678

unique proteins, revealed little overlap in species and protein composition

between the ships and contrasted with the metagenomic data in that ~80% of

classified and annotated proteins were of eukaryotic origin and dominated by

members of the Bacillariophyta, Cnidaria, Chordata and Arthropoda (data deposited

to the ProteomeXchange, identifier PXD000961). Within the shared metaproteome,

quantitative (18)O and iTRAQ analyses demonstrated a significantly greater

abundance of structural proteins from macroscopic eukaryotes on Ship-1 and diatom

photosynthesis proteins on Ship-2. Photosynthetic pigment composition and

elemental analyses confirmed that both biofilms were dominated by phototrophic

processes. These data begin to provide a better understanding of the complex

organismal and biomolecular composition of marine biofilms while highlighting

caveats in the interpretation of stand-alone environmental '-omics' datasets.

 

DOI: 10.1080/08927014.2014.977267

PMID: 25407927  [PubMed - indexed for MEDLINE]

 

 

92. PLoS One. 2013 Oct 22;8(10):e76724. doi: 10.1371/journal.pone.0076724.

eCollection 2013.

 

Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse

unexplored marine samples reveal varied bacterial community composition.

 

Aravindraja C(1), Viszwapriya D, Karutha Pandian S.

 

Author information:

(1)Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu,

India.

 

BACKGROUND: Bacterial community composition in the marine environment differs

from one geographical location to another. Reports that delineate the bacterial

diversity of different marine samples from geographically similar location are

limited. The present study aims to understand whether the bacterial community

compositions from different marine samples harbour similar bacterial diversity

since these are geographically related to each other.

METHODS AND PRINCIPAL FINDINGS: In the present study, 16S rRNA deep sequencing

analysis targeting V3 region was performed using Illumina bar coded sequencing. A

total of 22.44 million paired end reads were obtained from the metagenomic DNA of

Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of

Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has

the highest bacterial diversity and the least bacterial diversity was observed in

Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the

dominant taxa present in all the marine samples. Nearly 62-71% of rare species

were identified in all the samples and most of these rare species were unique to

a particular sample. Further taxonomic assignment at the phylum and genus level

revealed that the bacterial community compositions differ among the samples.

CONCLUSION: This is the first report that supports the fact that, bacterial

community composition is specific for specific samples irrespective of its

similar geographical location. Existence of specific bacterial community for each

sample may drive overall difference in bacterial structural composition of each

sample. Further studies like whole metagenomic sequencing will throw more

insights to the key stone players and its interconnecting metabolic pathways. In

addition, this is one of the very few reports that depicts the unexplored

bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment,

Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher

depths from uncharacterised coastal region of Palk Bay, India using next

generation sequencing technology.

 

DOI: 10.1371/journal.pone.0076724

PMCID: PMC3805540

PMID: 24167548  [PubMed - indexed for MEDLINE]

 

 

93. Nucleic Acids Res. 2013 Jan 7;41(1):e1. doi: 10.1093/nar/gks808. Epub 2012 Aug

28.

 

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and

next-generation sequencing-based diversity studies.

 

Klindworth A(1), Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO.

 

Author information:

(1)Max Planck Institute for Marine Microbiology, Microbial Genomics and

Bioinformatics Research Group, Celsiusstr 1, 28359 Bremen, Germany.

 

16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for

the cultivation-independent investigation of microbial diversity. The accuracy of

these analyses depends strongly on the choice of primers. The overall coverage

and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico

with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef

108 NR). Based on this evaluation a selection of 'best available' primer pairs

for Bacteria and Archaea for three amplicon size classes (100-400, 400-1000, ≥

1000 bp) is provided. The most promising bacterial primer pair

(S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was

experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA

amplicons with 16S rDNA fragments from directly sequenced metagenomes. The

results of this study may be used as a guideline for selecting primer pairs with

the best overall coverage and phylum spectrum for specific applications,

therefore reducing the bias in PCR-based microbial diversity studies.

 

DOI: 10.1093/nar/gks808

PMCID: PMC3592464

PMID: 22933715  [PubMed - indexed for MEDLINE]

 

 

94. PLoS One. 2013;8(3):e57782. doi: 10.1371/journal.pone.0057782. Epub 2013 Mar 4.

 

Detection of transient bacteraemia following dental extractions by 16S rDNA

pyrosequencing: a pilot study.

 

Benítez-Páez A(1), Álvarez M, Belda-Ferre P, Rubido S, Mira A, Tomás I.

 

Author information:

(1)Genomics and Health Department, Centre for Advanced Research in Public Health,

CSISP, Valencia, Spain.

 

OBJECTIVE: The current manuscript aims to determine the prevalence, duration and

bacterial diversity of bacteraemia following dental extractions using

conventional culture-dependent methods and 16S rDNA pyrosequencing.

METHODS: The study group included 8 patients undergoing dental extractions under

general anaesthesia. Peripheral venous blood samples were collected at baseline,

30 seconds and 15 minutes after the dental extractions. Blood samples were

analysed for bacteraemia applying conventional microbiological cultures under

aerobic and anaerobic conditions as well as pyrosequencing using universal

bacterial primers that target the 16S ribosomal DNA gene.

RESULTS: Transient bacteremia was detected by culture-based methods in one sample

at baseline time, in eight samples at 30 seconds, and in six samples at 15

minutes after surgical procedure; whereas bacteraemia was detected only in five

blood samples at 30 seconds after dental extraction by using pyrosequencing. By

applying conventional microbiological methods, a single microbial species was

detected in six patients, and Streptococcus viridans was the most frequently

cultured identified bacterium. By using pyrosequencing approaches however, the

estimated blood microbial diversity after dental extractions was 13.4±1.7

bacterial families and 22.8±1.1 genera per sample.

CONCLUSION: The application of 16S rDNA pyrosequencing underestimated the

prevalence and duration of bacteraemia following dental extractions, presumably

due to not reaching the minimum DNA required for PCR amplification. However, this

molecular technique, unlike conventional culture-dependent methods, revealed an

extraordinarily high bacterial diversity of post-extraction bacteraemia. We

propose that microorganisms recovered by culture may be only the tip of an

iceberg of a really diverse microbiota whose viability and potential

pathogenicity should be further studied.

 

DOI: 10.1371/journal.pone.0057782

PMCID: PMC3587628

PMID: 23469240  [PubMed - indexed for MEDLINE]

 

 

95. ISME J. 2015 Sep;9(9):2028-45. doi: 10.1038/ismej.2015.22. Epub 2015 Mar 3.

 

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading

enrichment cultures with 41 environmental samples.

 

Tan B(1), Fowler SJ(2), Abu Laban N(3), Dong X(4), Sensen CW(4), Foght J(1), Gieg

LM(2).

 

Author information:

(1)Department of Biological Sciences, University of Alberta, Edmonton, Alberta,

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

Alberta, Canada. (3)1] Department of Biological Sciences, University of Alberta,

Edmonton, Alberta, Canada [2] Department of Biological Sciences, University of

Calgary, Calgary, Alberta, Canada. (4)Visual Genomics Centre, Faculty of

Medicine, Calgary, Alberta, Canada.

 

Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs

and hydrocarbon-contaminated environments and thus warrants greater understanding

to improve current technologies for fossil fuel extraction and bioremediation. In

this study, three hydrocarbon-degrading methanogenic cultures established from

two geographically distinct environments and incubated with different hydrocarbon

substrates (added as single hydrocarbons or as mixtures) were subjected to

metagenomic and 16S rRNA gene pyrosequencing to test whether these differences

affect the genetic potential and composition of the communities. Enrichment of

different putative hydrocarbon-degrading bacteria in each culture appeared to be

substrate dependent, though all cultures contained both acetate- and H2-utilizing

methanogens. Despite differing hydrocarbon substrates and inoculum sources, all

three cultures harbored genes for hydrocarbon activation by fumarate addition

(bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for

associated downstream pathways (bbs, bcr, bam), though the cultures incubated

with hydrocarbon mixtures contained a broader diversity of fumarate addition

genes. A comparative metagenomic analysis of the three cultures showed that they

were functionally redundant despite their enrichment backgrounds, sharing

multiple features associated with syntrophic hydrocarbon conversion to methane.

In addition, a comparative analysis of the culture metagenomes with those of 41

environmental samples (containing varying proportions of methanogens) showed that

the three cultures were functionally most similar to each other but distinct from

other environments, including hydrocarbon-impacted environments (for example, oil

sands tailings ponds and oil-affected marine sediments). This study provides a

basis for understanding key functions and environmental selection in methanogenic

hydrocarbon-associated communities.

 

DOI: 10.1038/ismej.2015.22

PMCID: PMC4542035

PMID: 25734684  [PubMed - indexed for MEDLINE]

 

 

96. Microbiologyopen. 2013 Apr;2(2):276-83. doi: 10.1002/mbo3.73. Epub 2013 Feb 17.

 

Analysis of the bacterial communities associated with two ant-plant symbioses.

 

Seipke RF(1), Barke J, Heavens D, Yu DW, Hutchings MI.

 

Author information:

(1)School of Biological Sciences, University of East Anglia, Norwich Research

Park, Norwich NR4 7TJ, United Kingdom. r.seipke@uea.ac.uk

 

Insect fungiculture is practiced by ants, termites, beetles, and gall midges and

it has been suggested to be widespread among plant-ants. Some of the insects

engaged in fungiculture, including attine ants and bark beetles, are known to use

symbiotic antibiotic-producing actinobacteria to protect themselves and their

fungal cultivars against infection. In this study, we analyze the bacterial

communities on the cuticles of the plant-ant genera Allomerus and Tetraponera

using deep sequencing of 16S rRNA. Allomerus ants cultivate fungus as a building

material to strengthen traps for prey, while Tetraponera ants cultivate fungus as

a food source. We report that Allomerus and Tetraponera microbiomes contain >75%

Proteobacteria and remarkably the bacterial phyla that dominate their cuticular

microbiomes are very similar despite their geographic separation (South America

and Africa, respectively). Notably, antibiotic-producing actinomycete bacteria

represent a tiny fraction of the cuticular microbiomes of both Allomerus and

Tetraponera spp. and instead they are dominated by γ-proteobacteria Erwinia and

Serratia spp. Both these phyla are known to contain antibiotic-producing species

which might therefore play a protective role in these ant-plant systems.

 

© 2013 The Authors. Published by Blackwell Publishing Ltd.

 

DOI: 10.1002/mbo3.73

PMCID: PMC3633351

PMID: 23417898  [PubMed - indexed for MEDLINE]

 

 

97. ISME J. 2014 Feb;8(2):478-91. doi: 10.1038/ismej.2013.159. Epub 2013 Sep 12.

 

Making a living while starving in the dark: metagenomic insights into the energy

dynamics of a carbonate cave.

 

Ortiz M(1), Legatzki A(1), Neilson JW(1), Fryslie B(2), Nelson WM(3), Wing RA(4),

Soderlund CA(3), Pryor BM(4), Maier RM(1).

 

Author information:

(1)Department of Soil, Water and Environmental Science, University of Arizona,

Tucson, AZ, USA. (2)Department of Computer Science, University of Arizona,

Tucson, AZ, USA. (3)BIO5 Institute, Tucson, AZ, USA. (4)Department of Plant

Sciences, University of Arizona, Tucson, AZ, USA.

 

Carbonate caves represent subterranean ecosystems that are largely devoid of

phototrophic primary production. In semiarid and arid regions, allochthonous

organic carbon inputs entering caves with vadose-zone drip water are minimal,

creating highly oligotrophic conditions; however, past research indicates that

carbonate speleothem surfaces in these caves support diverse, predominantly

heterotrophic prokaryotic communities. The current study applied a metagenomic

approach to elucidate the community structure and potential energy dynamics of

microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a

carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a

speleothem metagenome revealed a community genetically adapted to low-nutrient

conditions with indications that a nitrogen-based primary production strategy is

probable, including contributions from both Archaea and Bacteria. Genes for all

six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes

representative of the Calvin-Benson-Bassham cycle were over-represented in

Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and

deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be

significantly more abundant in the cave communities than in soils above the cave.

MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads

found Thaumarchaeota to be the third most abundant phylum in the community, and

identified taxonomic associations to this phylum for indicator genes

representative of multiple CO2-fixation pathways. The results revealed that this

oligotrophic subterranean environment supports a unique chemoautotrophic

microbial community with potentially novel nutrient cycling strategies. These

strategies may provide key insights into other ecosystems dominated by

oligotrophy, including aphotic subsurface soils or aquifers and photic systems

such as arid deserts.

 

DOI: 10.1038/ismej.2013.159

PMCID: PMC3906820

PMID: 24030597  [PubMed - indexed for MEDLINE]

 

 

98. Arch Dis Child Fetal Neonatal Ed. 2013 Jul;98(4):F334-40. doi:

10.1136/archdischild-2012-303035. Epub 2013 Jan 8.

 

The individual-specific and diverse nature of the preterm infant microbiota.

 

Barrett E(1), Kerr C, Murphy K, O'Sullivan O, Ryan CA, Dempsey EM, Murphy BP,

O'Toole PW, Cotter PD, Fitzgerald GF, Ross RP, Stanton C.

 

Author information:

(1)Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy,

County Cork, Ireland.

 

OBJECTIVE: To examine the composition of the evolving microbiota of preterm

infants at weeks 2 and 4 of life.

SETTINGS: The paediatric intensive care unit of the Cork University Maternity

Hospital.

METHODS: The microbial diversity of faecal samples from 10 preterm infants was

determined using 16S rRNA amplicon pyrosequencing technology.

RESULTS: In total, 452 863 sequences were obtained from 20 faecal samples

collected from 10 preterm infants, allowing a level of analysis not previously

reported. The preterm infant microbiota samples were dominated by Proteobacteria

(46%), followed by Firmicutes (45%), while the phyla Actinobacteria (2%) and

Bacteroidetes (7%) were detected at much lower levels at week 2 of life. This

colonisation pattern was similar at week 4 of life. At the family level,

Enterobacteriaceae were detected at 50% and 58% at weeks 2 and 4, respectively.

The preterm infants were characterised by a lack of detectable Bifidobacterium

and Lactobacillus genera commonly associated with the infant gut. In addition to

the dominance of the Proteobacteria, a high level of interindividual variation

was observed, indeed the relative proportions of different phyla, families and

genera in different infants ranged from <1% to >90%.

CONCLUSIONS: The results indicate that in addition to an uncharacteristic

microbiota relative to that reported for healthy term infants, there was a large

interindividual variation in the faecal microbiota diversity of preterm infants

suggesting that the preterm microbiota is individual-specific and does not

display a uniformity among infants.

 

DOI: 10.1136/archdischild-2012-303035

PMID: 23303303  [PubMed - indexed for MEDLINE]

 

 

99. Appl Microbiol Biotechnol. 2013 Mar;97(6):2681-90. doi:

10.1007/s00253-012-4082-4. Epub 2012 May 5.

 

Bacterial communities in different sections of a municipal wastewater treatment

plant revealed by 16S rDNA 454 pyrosequencing.

 

Ye L(1), Zhang T.

 

Author information:

(1)Environmental Biotechnology Lab, Department of Civil Engineering, The

University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.

 

In this study, we successfully demonstrated that 454 pyrosequencing was a

powerful approach for investigating the bacterial communities in the activated

sludge, digestion sludge, influent, and effluent samples of a full scale

wastewater treatment plant treating saline sewage. For each sample, 18,808

effective sequences were selected and utilized to do the bacterial diversity and

abundance analysis. In total, 2,455, 794, 1,667, and 1,932 operational taxonomic

units were obtained at 3 % distance cutoff in the activated sludge, digestion

sludge, influent, and effluent samples, respectively. The corresponding most

dominant classes in the four samples are Alphaproteobacteria, Thermotogae,

Deltaproteobacteria, and Gammaproteobacteria. About 67 % sequences in the

digestion sludge sample were found to be affiliated with the Thermotogales order.

Also, these sequences were assigned into a recently proposed genus Kosmotoga by

the Ribosomal Database Project classifier. In the effluent sample, we found high

abundance of Mycobacterium and Vibrio, which are genera containing pathogenic

bacteria. Moreover, in this study, we proposed a method to differentiate the

"gene percentage" and "cell percentage" by using Ribosomal RNA Operon Copy Number

Database.

 

DOI: 10.1007/s00253-012-4082-4

PMCID: PMC3586070

PMID: 22555912  [PubMed - indexed for MEDLINE]

 

 

100. Sci Rep. 2015 Sep 22;5:14266. doi: 10.1038/srep14266.

 

An integrated insight into the response of sedimentary microbial communities to

heavy metal contamination.

 

Yin H(1,)(2), Niu J(1,)(2), Ren Y(3), Cong J(1,)(2), Zhang X(4,)(5), Fan

F(6,)(5), Xiao Y(1,)(2), Zhang X(1,)(2), Deng J(7), Xie M(7), He Z(7), Zhou

J(7,)(8,)(9), Liang Y(1,)(2), Liu X(1,)(2).

 

Author information:

(1)School of Minerals Processing and Bioengineering, Central South University,

Changsha 410083, China. (2)Key laboratory of Biometallurgy, Ministry of

Education, Changsha 410083, China. (3)College of Food Science and Technology,

Hunan Agricultural University, Changsha 410083, China. (4)Key Laboratory of

Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing

100081, China. (5)Institute of Agricultural Resources and Regional Planning,

Chinese Academy of Agricultural Sciences, Beijing 100081, China. (6)Key

Laboratory of Plant Nutrition and Fertilizer, Beijing 100081, China. (7)Institute

for Environmental Genomics and Department of Botany and Microbiology, University

of Oklahoma, Norman 73019, USA. (8)School of Environment, Tsinghua University,

Beijing 100084, China. (9)Earth Sciences Division, Lawrence Berkeley National

Laboratory, Berkeley 94710, USA.

 

Response of biological communities to environmental stresses is a critical issue

in ecology, but how microbial communities shift across heavy metal gradients

remain unclear. To explore the microbial response to heavy metal contamination

(e.g., Cr, Mn, Zn), the composition, structure and functional potential of

sedimentary microbial community were investigated by sequencing of 16S rRNA gene

amplicons and a functional gene microarray. Analysis of 16S rRNA sequences

revealed that the composition and structure of sedimentary microbial communities

changed significantly across a gradient of heavy metal contamination, and the

relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota,

but lower for Proteobacteria and Actinobacteria in highly contaminated samples.

Also, molecular ecological network analysis of sequencing data indicated that

their possible interactions might be enhanced in highly contaminated communities.

Correspondently, key functional genes involved in metal homeostasis (e.g., chrR,

metC, merB), carbon metabolism, and organic remediation showed a higher abundance

in highly contaminated samples, indicating that bacterial communities in

contaminated areas may modulate their energy consumption and organic remediation

ability. This study indicated that the sedimentary indigenous microbial community

may shift the composition and structure as well as function priority and

interaction network to increase their adaptability and/or resistance to

environmental contamination.

 

DOI: 10.1038/srep14266

PMCID: PMC4585741

PMID: 26391875  [PubMed - indexed for MEDLINE]

 

 

 

 

36. Front Microbiol. 2016 Jul 19;7:1122. doi: 10.3389/fmicb.2016.01122. eCollection

2016.

 

Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and

Fermentation Response in the Rumen of Cattle.

 

Martinez-Fernandez G(1), Denman SE(1), Yang C(2), Cheung J(1), Mitsumori M(3),

McSweeney CS(1).

 

Author information:

(1)CSIRO, Agriculture and Food, Queensland Bioscience Precinct St Lucia, QLD,

Australia. (2)Institute of Dairy Science, MoE Key Laboratory of Molecular Animal

Nutrition, College of Animal Sciences, Zhejiang University Hangzhou, China.

(3)NARO Institute of Livestock and Grassland Science Tsukuba, Japan.

 

Management of metabolic hydrogen ([H]) in the rumen has been identified as an

important consideration when reducing ruminant CH4 emissions. However, little is

known about hydrogen flux and microbial rumen population responses to CH4

inhibition when animals are fed with slowly degradable diets. The effects of the

anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology,

and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman

steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate

diet (60:40) with increasing levels (low, mid, and high) of chloroform in a

cyclodextrin matrix. The increasing levels of chloroform resulted in an increase

in H2 expelled as CH4 production decreased with no effect on dry matter intakes.

The amount of expelled H2 per mole of decreased methane, was lower for the hay

diet suggesting a more efficient redirection of hydrogen into other microbial

products compared with hay:concentrate diet. A shift in rumen fermentation toward

propionate and branched-chain fatty acids was observed for both diets. Animals

fed with the hay:concentrate diet had both higher formate concentration and H2

expelled than those fed only roughage hay. Metabolomic analyses revealed an

increase in the concentration of amino acids, organic, and nucleic acids in the

fluid phase for both diets when methanogenesis was inhibited. These changes in

the rumen metabolism were accompanied by a shift in the microbiota with an

increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and

Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned

to Prevotella were promoted under chloroform treatment. These bacteria may be

partly responsible for the increase in amino acids and propionate in the rumen.

No significant changes were observed for abundance of fibrolytic bacteria,

protozoa, and fungi, which suggests that fiber degradation was not impaired. The

observed 30% decrease in methanogenesis did not adversely affect rumen metabolism

and the rumen microbiota was able to adapt and redirect [H] into other microbial

end-products for both diets. However, it is also required dietary supplements or

microbial treatments to capture the additional H2 expelled by the animal to

further improve rumen digestive efficiency.

 

DOI: 10.3389/fmicb.2016.01122

PMCID: PMC4949212

PMID: 27486452  [PubMed]

 

 

37. Elife. 2013 Nov 5;2:e01202. doi: 10.7554/eLife.01202.

 

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility

to arthritis.

 

Scher JU(1), Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T,

Cerundolo V, Pamer EG, Abramson SB, Huttenhower C, Littman DR.

 

Author information:

(1)Department of Medicine, New York University School of Medicine and Hospital

for Joint Diseases, New York, United States.

 

Comment in

    Nat Rev Microbiol. 2014 Jan;12(1):5.

    Elife. 2013;2:e01608.

    Nat Rev Rheumatol. 2014 Jan;10(1):2.

 

Rheumatoid arthritis (RA) is a prevalent systemic autoimmune disease, caused by a

combination of genetic and environmental factors. Animal models suggest a role

for intestinal bacteria in supporting the systemic immune response required for

joint inflammation. Here we performed 16S sequencing on 114 stool samples from

rheumatoid arthritis patients and controls, and shotgun sequencing on a subset of

44 such samples. We identified the presence of Prevotella copri as strongly

correlated with disease in new-onset untreated rheumatoid arthritis (NORA)

patients. Increases in Prevotella abundance correlated with a reduction in

Bacteroides and a loss of reportedly beneficial microbes in NORA subjects. We

also identified unique Prevotella genes that correlated with disease. Further,

colonization of mice revealed the ability of P. copri to dominate the intestinal

microbiota and resulted in an increased sensitivity to chemically induced

colitis. This work identifies a potential role for P. copri in the pathogenesis

of RA. DOI: http://dx.doi.org/10.7554/eLife.01202.001.

 

DOI: 10.7554/eLife.01202

PMCID: PMC3816614

PMID: 24192039  [PubMed - indexed for MEDLINE]

 

 

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

 

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

 

Li C(1,)(2), Chng KR(1), Boey EJ(1), Ng AH(1), Wilm A(1), Nagarajan N(3,)(4).

 

Author information:

(1)Genome Institute of Singapore, Singapore, 138672, Singapore. (2)Department of

Computer Science, National University of Singapore, Singapore, 117417, Singapore.

(3)Genome Institute of Singapore, Singapore, 138672, Singapore.

nagarajann@gis.a-star.edu.sg. (4)Department of Computer Science, National

University of Singapore, Singapore, 117417, Singapore.

nagarajann@gis.a-star.edu.sg.

 

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.

 

DOI: 10.1186/s13742-016-0140-7

PMCID: PMC4970289

PMID: 27485345  [PubMed - in process]

 

 

39. Ecology. 2016 May;97(5):1307-18.

 

Climate and edaphic controllers influence rhizosphere community assembly for a

wild annual grass.

 

Nuccio EE, Anderson-Furgeson J, Estera KY, Pett-Ridge J, De Valpine P, Brodie EL,

Firestone MK.

 

The interface between roots and soil, known as the rhizosphere, is a dynamic

habitat in the soil ecosystem. Unraveling the factors that control rhizosphere

community assembly is a key starting point for understanding the diversity of

plant-microbial interactions that occur in soil. The goals of this study were to

determine how environmental factors shape rhizosphere microbial communities, such

as local soil characteristics and the regional climate, and to determine the

relative influence of the rhizosphere on microbial community assembly compared to

the pressures imposed by the local and regional environment. We identified the

bacteria present in the soil immediately adjacent to the roots of wild oat (A

vena spp.) in three California grasslands using deep Illumina 16S sequencing.

Rhizosphere communities were more similar to each other than to the surrounding

soil communities from which they were derived, despite the fact that the

grasslands studied were separated by hundreds of kilometers. The rhizosphere was

the dominant factor structuring bacterial community composition (38% variance

explained), and was comparable in magnitude to the combined local and regional

effects (22% and 21%, respectively). Rhizosphere communities were most influenced

by factors related to the regional climate (soil moisture and temperature), while

background soil communities were more influenced by soil characteristics (pH,

CEC, exchangeable cations, clay content). The Avena core microbiome was strongly

phylogenetically clustered according to the metrics NRI and NTI, which indicates

that selective processes likely shaped these communities. Furthermore, 17% of

these taxa were not detectable in the background soil, even with a robust

sequencing depth of approximately 70,000 sequences per sample. These results

support the hypothesis that roots select less abundant or possibly rare

populations in the soil microbial community, which appear to be lineages of

bacteria that have made a physiological tradeoff for rhizosphere competence at

the expense of their competitiveness in non-rhizosphere soil.

 

 

PMID: 27349106  [PubMed - indexed for MEDLINE]

 

 

40. Anaerobe. 2016 Apr;38:130-7. doi: 10.1016/j.anaerobe.2015.10.006. Epub 2015 Oct

19.

 

Comparison of culture-dependent and independent approaches to characterize fecal

bifidobacteria and lactobacilli.

 

Quartieri A(1), Simone M(1), Gozzoli C(1), Popovic M(1), D'Auria G(2), Amaretti

A(1), Raimondi S(1), Rossi M(3).

 

Author information:

(1)Department of Life Sciences, University of Modena and Reggio Emilia, Modena,

Italy. (2)Genómica y Salud, Fundación para el Fomento de la Investigación

Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain. (3)Department

of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

Electronic address: maddalena.rossi@unimore.it.

 

Different culture-dependent and independent methods were applied to investigate

the population of bifidobacteria and lactobacilli in the feces of five healthy

subjects. Bacteria were isolated on MRS, a complex medium supporting growth of

lactobacilli and bifidobacteria, and on three selective media for bifidobacteria

and two for lactobacilli. Taxonomic characterization of the isolates was carried

out by RAPD-PCR and partial 16S sequencing. The selectivity of genus-specific

media was also investigated by challenging colonies from MRS plates to grow onto

each medium. In parallel, a quantitative and qualitative description of

bifidobacteria and lactic acid bacteria was obtained by FISH, qPCR, TRFLP, and

16S rRNA gene sequencing. Bifidobacteria did not fail to grow on their specific

media and were easily isolated and enumerated, showing comparable quantitative

data among culture-dependent and -independent techniques. The Bifidobacterium

species identified on plates and those extracted from TRFLP and 16S rRNA gene

sequencing were mostly overlapping. Selective media for lactobacilli gave

unsuitable results, being too stringent or too permissive. The quantification of

lactobacilli through selective plates, qPCR, FISH, and 16S rRNA gene sequencing

gave unreliable results. Therefore, unlike bifidobacteria, intestinal

lactobacilli are still problematic in terms of quantification and accurate

profiling at level of species and possibly of strains by both culture-dependent

and culture-independent techniques.

 

Copyright © 2015 Elsevier Ltd. All rights reserved.

 

DOI: 10.1016/j.anaerobe.2015.10.006

PMID: 26481833  [PubMed - in process]

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

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Environ Sci Pollut Res Int. 2016 Jul;23(13):13245-54. doi: 10.1007/s11356-016-6474-y. Epub 2016 Mar 29.

Influence of zinc nanoparticles on survival of worms Eisenia fetida and taxonomic diversity of the gut microflora.

Yausheva Е1, Sizova Е2,3, Lebedev S2,3, Skalny A2, Miroshnikov S3, Plotnikov A4, Khlopko Y4, Gogoleva N5, Cherkasov S4.

Author information

Abstract

The study was conducted to examine the effect of zinc nanoparticles on survival of worms Eisenia fetida and composition of the gut microflora. Analysis of the survival data has shown that the introduction of high doses of the nanoparticles causes death of worms in the second group with 35 % mortality rate and activates protective mechanisms realized as mucous film. DNA from the worm guts was extracted and 16S metagenomic sequencing was fulfilled using MiSeq (Illumina). Regarding the gut microflora of worms in the control group, high diversity of microorganisms (303 OTUs) was noted. Most of those belong to the taxa Firmicutes (51.9 % of the total high-quality united reads), Proteobacteria (24.1 % of the total), and Actinobacteria (13.3 % of the total), which were represented by numerous species of gen. Clostridium (C. saccharobutylicum, C. saccharoperbutylacetonicum, C. beijerinckii), gen. Pseudomonas (P. hydrogenovora, P. aeruginosa, and P. putida), gen. Bacillus (B. megaterium, B. silvestris), gen. Cellulomonas (B. megaterium, B. silvestris), and other numerically smaller genera. Adding of zinc nanoparticles to the substrate decreased the diversity of bacteria (78 OTUs) as well as percentage of bacteria belonging to the taxon Firmicutes (-41.6 %) and increased the proportion of Proteobacteria due to growth in abundance of gen. Verminephrobacter (+46 %) and gen. Ochrobactrum (+19.5 %).

KEYWORDS:

16S metagenome; Eisenia fetida; High-throughput sequencing; Microcrystalline cellulose; Microflora; Nanoparticles; Taxa; Zinc

PMID: 27023811 DOI: 10.1007/s11356-016-6474-y

[PubMed - in process]

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26.

Sci Rep. 2015 Jun 12;5:10044. doi: 10.1038/srep10044.

Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing.

Chao Y1, Mao Y2, Wang Z3, Zhang T2.

Author information

Abstract

The development of biofilms in drinking water (DW) systems may cause various problems to water quality. To investigate the community structure of biofilms on different pipe materials and the global/specific metabolic functions of DW biofilms, PCR-based 454 pyrosequencing data for 16S rRNA genes and Illumina metagenomic data were generated and analysed. Considerable differences in bacterial diversity and taxonomic structure were identified between biofilms formed on stainless steel and biofilms formed on plastics, indicating that the metallic materials facilitate the formation of higher diversity biofilms. Moreover, variations in several dominant genera were observed during biofilm formation. Based on PCA analysis, the global functions in the DW biofilms were similar to other DW metagenomes. Beyond the global functions, the occurrences and abundances of specific protective genes involved in the glutathione metabolism, the SoxRS system, the OxyR system, RpoS regulated genes, and the production/degradation of extracellular polymeric substances were also evaluated. A near-complete and low-contamination draft genome was constructed from the metagenome of the DW biofilm, based on the coverage and tetranucleotide frequencies, and identified as a Bradyrhizobiaceae-like bacterium according to a phylogenetic analysis. Our findings provide new insight into DW biofilms, especially in terms of their metabolic functions.

TRIAL REGISTRATION:

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PMID: 26067561 PMCID: PMC4464384 DOI: 10.1038/srep10044

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27.

PLoS One. 2015 Jun 2;10(6):e0128711. doi: 10.1371/journal.pone.0128711. eCollection 2015.

Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach.

Jalali S1, Kohli S2, Latka C3, Bhatia S4, Vellarikal SK5, Sivasubbu S5, Scaria V1, Ramachandran S1.

Author information

Abstract

Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%), bacteria (9%), viruses and archae (~1%). We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents.

TRIAL REGISTRATION:

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PMID: 26035208 PMCID: PMC4452720 DOI: 10.1371/journal.pone.0128711

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28.

Microb Ecol. 2015 Oct;70(3):701-9. doi: 10.1007/s00248-015-0611-x. Epub 2015 Apr 26.

Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome.

Wang Z1,2, Liu L1,3, Guo F1, Zhang T4.

Author information

Abstract

Biotreatment processes fed with coking wastewater often encounter insufficient removal of pollutants, such as ammonia, phenols, and polycyclic aromatic hydrocarbons (PAHs), especially for cyanides. However, only a limited number of bacterial species in pure cultures have been confirmed to metabolize cyanides, which hinders the improvement of these processes. In this study, a microbial community of activated sludge enriched in a coking wastewater treatment plant was analyzed using 454 pyrosequencing and Illumina sequencing to characterize the potential cyanide-degrading bacteria. According to the classification of these pyro-tags, targeting V3/V4 regions of 16S rRNA gene, half of them were assigned to the family Xanthomonadaceae, implying that Xanthomonadaceae bacteria are well-adapted to coking wastewater. A nearly complete draft genome of the dominant bacterium was reconstructed from metagenome of this community to explore cyanide metabolism based on analysis of the genome. The assembled 16S rRNA gene from this draft genome showed that this bacterium was a novel species of Thermomonas within Xanthomonadaceae, which was further verified by comparative genomics. The annotation using KEGG and Pfam identified genes related to cyanide metabolism, including genes responsible for the iron-harvesting system, cyanide-insensitive terminal oxidase, cyanide hydrolase/nitrilase, and thiosulfate:cyanide transferase. Phylogenetic analysis showed that these genes had homologs in previously identified genomes of bacteria within Xanthomonadaceae and even presented similar gene cassettes, thus implying an inherent cyanide-decomposing potential. The findings of this study expand our knowledge about the bacterial degradation of cyanide compounds and will be helpful in the remediation of cyanides contamination.

TRIAL REGISTRATION:

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KEYWORDS:

Activated sludge; Coking wastewater; Cyanides; Metagenome; Thermomonas

PMID: 25910603 DOI: 10.1007/s00248-015-0611-x

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29.

Microb Cell Fact. 2015 Mar 14;14:33. doi: 10.1186/s12934-015-0218-4.

Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing.

Guo J1,2, Peng Y3, Ni BJ4, Han X5,6, Fan L7, Yuan Z8.

Author information

Abstract

BACKGROUND:

Anaerobic digestion has been widely applied to treat the waste activated sludge from biological wastewater treatment and produce methane for biofuel, which has been one of the most efficient solutions to both energy crisis and environmental pollution challenges. Anaerobic digestion sludge contains highly complex microbial communities, which play crucial roles in sludge treatment. However, traditional approaches based on 16S rRNA amplification or fluorescent in situ hybridization cannot completely reveal the whole microbial community structure due to the extremely high complexity of the involved communities. In this sense, the next-generation high-throughput sequencing provides a powerful tool for dissecting microbial community structure and methane-producing pathways in anaerobic digestion.

RESULTS:

In this work, the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment plant. Over 3.0 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. Taxonomic analysis by MG-RAST server indicated that overall bacteria were dominant (~93%) whereas a considerable abundance of archaea (~6%) were also detected in the anaerobic digestion sludge. The most abundant bacterial populations were found to be Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Key microorganisms and related pathways involved in methanogenesis were further revealed. The dominant proliferation of Methanosaeta and Methanosarcina, together with the functional affiliation of enzymes-encoding genes (acetate kinase (AckA), phosphate acetyltransferase (PTA), and acetyl-CoA synthetase (ACSS)), suggested that the acetoclastic methanogenesis is the dominant methanogenesis pathway in the full-scale anaerobic digester.

CONCLUSIONS:

In short, the metagenomic sequencing study of this work successfully dissected the detail microbial community structure and the dominated methane-producing pathways of a full-scale anaerobic digester. The knowledge garnered would facilitate to develop more efficient full-scale anaerobic digestion systems to achieve high-rate waste sludge treatment and methane production.

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PMID: 25880314 PMCID: PMC4381419 DOI: 10.1186/s12934-015-0218-4

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Appl Biochem Biotechnol. 2015 Apr;175(7):3258-70. doi: 10.1007/s12010-015-1491-8. Epub 2015 Feb 10.

Metagenomic analysis of the sludge microbial community in a lab-scale denitrifying phosphorus removal reactor.

Lv XM1, Shao MF, Li J, Li CL.

Author information

Abstract

Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. In the present study, the metagenome of denitrifying phosphorus removal sludge from a lab-scale anaerobic-anoxic SBR was generated by Illumina sequencing to study the microbial community. Compared with the aerobic phosphorus removal sludge, the denitrifying phosphorus removal sludge demonstrated quite similar microbial community profile and microbial diversity with sludge from Aalborg East EBPR WWTP. Proteobacteria was the most dominant phylum; within Proteobacteria, β-Proteobacteria was the most dominant class, followed by α-, γ-, δ-, and ε-Proteobacteria. The genes involved in phosphate metabolism and biofilm formation reflected the selective pressure of the phosphorus removal process. Moreover, ppk sequence from DPAO was outside the Accumulibacter clusters, which suggested different core phosphorus removal bacteria in denitrifying and aerobic phosphorus removal systems. In a summary, putative DPAO might be a novel genus that is closely related between Accumulibacter and Dechloromonas within Rhodocyclus. The microbial community and metabolic profiles achieved in this study will eventually help to improve the understanding of key microorganisms and the entire community in order to improve the phosphorus removal efficiency of EBPR processes.

TRIAL REGISTRATION:

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PMID: 25820294 DOI: 10.1007/s12010-015-1491-8

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16s rRNA Sequencing with MR DNA

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

 

 

 

 

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