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Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing. PLoS One 2014; 9:e105592. [PMID: 25144201 PMCID: PMC4140814 DOI: 10.1371/journal.pone.0105592] [Citation(s) in RCA: 788] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/26/2014] [Indexed: 01/03/2023] Open
Abstract
For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace × Large white × Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (± 20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.
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Inoue D, Pang J, Matsuda M, Sei K, Nishida K, Ike M. Development of a whole community genome amplification-assisted DNA microarray method to detect functional genes involved in the nitrogen cycle. World J Microbiol Biotechnol 2014; 30:2907-15. [DOI: 10.1007/s11274-014-1718-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/31/2014] [Indexed: 11/28/2022]
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On the Usefulness of Circulating Bacterial 16S rDNA as a Marker of Microbial Translocation in HIV-1–Infected Patients. J Acquir Immune Defic Syndr 2014; 66:e87-9. [DOI: 10.1097/qai.0000000000000188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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54
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Halophilic microorganisms are responsible for the rosy discolouration of saline environments in three historical buildings with mural paintings. PLoS One 2014; 9:e103844. [PMID: 25084531 PMCID: PMC4118916 DOI: 10.1371/journal.pone.0103844] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 07/02/2014] [Indexed: 01/31/2023] Open
Abstract
A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory.
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Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol 2014; 5:219. [PMID: 24904535 PMCID: PMC4033041 DOI: 10.3389/fmicb.2014.00219] [Citation(s) in RCA: 780] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/26/2014] [Indexed: 01/17/2023] Open
Abstract
Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.
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Affiliation(s)
- David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Stefanie Widder
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
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56
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Targeted and highly multiplexed detection of microorganisms by employing an ensemble of molecular probes. Appl Environ Microbiol 2014; 80:4153-61. [PMID: 24795371 DOI: 10.1128/aem.00666-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vast majority of microscopic life on earth consists of microbes that do not grow in laboratory culture. To profile the microbial diversity in environmental and clinical samples, we have devised and employed molecular probe technology, which detects and identifies bacteria that do and do not grow in culture. The only requirement is a short sequence of contiguous bases (currently 60 bases) unique to the genome of the organism of interest. The procedure is relatively fast, inexpensive, customizable, robust, and culture independent and uses commercially available reagents and instruments. In this communication, we report improving the specificity of the molecular probes substantially and increasing the complexity of the molecular probe set by over an order of magnitude (>1,200 probes) and introduce a new final readout method based upon Illumina sequencing. In addition, we employed molecular probes to identify the bacteria from vaginal swabs and demonstrate how a deliberate selection of molecular probes can identify less abundant bacteria even in the presence of much more abundant species.
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57
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Effects of temperature on microbial succession and metabolite change during saeu-jeot fermentation. Food Microbiol 2014; 38:16-25. [DOI: 10.1016/j.fm.2013.08.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/03/2013] [Accepted: 08/10/2013] [Indexed: 11/18/2022]
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Teles R, Teles F, Frias-Lopez J, Paster B, Haffajee A. Lessons learned and unlearned in periodontal microbiology. Periodontol 2000 2014; 62:95-162. [PMID: 23574465 PMCID: PMC3912758 DOI: 10.1111/prd.12010] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Periodontal diseases are initiated by bacterial species living in polymicrobial biofilms at or below the gingival margin and progress largely as a result of the inflammation elicited by specific subgingival species. In the past few decades, efforts to understand the periodontal microbiota have led to an exponential increase in information about biofilms associated with periodontal health and disease. In fact, the oral microbiota is one of the best-characterized microbiomes that colonize the human body. Despite this increased knowledge, one has to ask if our fundamental concepts of the etiology and pathogenesis of periodontal diseases have really changed. In this article we will review how our comprehension of the structure and function of the subgingival microbiota has evolved over the years in search of lessons learned and unlearned in periodontal microbiology. More specifically, this review focuses on: (i) how the data obtained through molecular techniques have impacted our knowledge of the etiology of periodontal infections; (ii) the potential role of viruses in the etiopathogenesis of periodontal diseases; (iii) how concepts of microbial ecology have expanded our understanding of host-microbe interactions that might lead to periodontal diseases; (iv) the role of inflammation in the pathogenesis of periodontal diseases; and (v) the impact of these evolving concepts on therapeutic and preventive strategies to periodontal infections. We will conclude by reviewing how novel systems-biology approaches promise to unravel new details of the pathogenesis of periodontal diseases and hopefully lead to a better understanding of their mechanisms.
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59
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Mavengere NR, Ellis AG, Le Roux JJ. Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb. Int J Syst Evol Microbiol 2014; 64:1906-1912. [PMID: 24599894 DOI: 10.1099/ijs.0.057067-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study to investigate the diversity of rhizobia associated with native legumes in South Africa's Cape Floristic Region, a Gram-negative bacterium designated VG1C(T) was isolated from the root nodules of Aspalathus abietina Thunb. Based on phylogenetic analyses of the 16S rRNA and recA genes, VG1C(T) belongs to the genus Burkholderia, with the highest degree of sequence similarity to the type strain of Burkholderia sediminicola (98.5% and 98%, respectively). The DNA G+C content of strain VG1C(T) was 60.1 mol%, and DNA-DNA relatedness values to the type strain of closely related species were found to be substantially lower than 70%. As evidenced by results of genotypic, phenotypic and chemotaxonomic tests provided here, we conclude that isolate VG1C(T) represents a novel rhizosphere-associated species in the genus Burkholderia, for which the name Burkholderia aspalathi sp. nov. is proposed, with the type strain VG1C(T) ( = DSM 27239(T) = LMG 27731(T)).
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Affiliation(s)
- Natasha R Mavengere
- Centre for Invasion Biology, Department of Botany and Zoology, Natural Sciences Building, Private Bag X1, Stellenbosch University, Matieland 7602, Western Cape, South Africa
| | - Allan G Ellis
- Department of Botany and Zoology, Natural Sciences Building, Private Bag X1, Stellenbosch University, Matieland 7602, Western Cape, South Africa
| | - Johannes J Le Roux
- Centre for Invasion Biology, Department of Botany and Zoology, Natural Sciences Building, Private Bag X1, Stellenbosch University, Matieland 7602, Western Cape, South Africa
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60
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Mehta CM, Palni U, Franke-Whittle IH, Sharma AK. Compost: its role, mechanism and impact on reducing soil-borne plant diseases. WASTE MANAGEMENT (NEW YORK, N.Y.) 2014; 34:607-22. [PMID: 24373678 DOI: 10.1016/j.wasman.2013.11.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/28/2013] [Accepted: 11/28/2013] [Indexed: 05/14/2023]
Abstract
Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.
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Affiliation(s)
- C M Mehta
- Department of Biological Sciences, College of Basic Science and Humanities, G. B. P. U. A. & T. Pantnagar, U.S. Nagar, Uttarakhand, India; Department of Botany, D.S.B. Campus, Kumaun University Nainital, Uttarakhand, India
| | - Uma Palni
- Department of Botany, D.S.B. Campus, Kumaun University Nainital, Uttarakhand, India
| | - I H Franke-Whittle
- Leopold-Franzens University, Institute of Microbiology, Technikerstraße 25, 6020 Innsbruck, Austria
| | - A K Sharma
- Department of Biological Sciences, College of Basic Science and Humanities, G. B. P. U. A. & T. Pantnagar, U.S. Nagar, Uttarakhand, India.
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61
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Laverock B, Tait K, Gilbert JA, Osborn AM, Widdicombe S. Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:113-21. [PMID: 24596269 PMCID: PMC4208606 DOI: 10.1111/1758-2229.12115] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/11/2013] [Indexed: 05/13/2023]
Abstract
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over the temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.
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Affiliation(s)
- B Laverock
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
- Department of Animal and Plant Sciences, University of SheffieldSheffield, S10 2TN, UK
- School of Plant Biology and the UWA Oceans Institute, University of Western AustraliaCrawley, WA, 6009, Australia
| | - K Tait
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
| | - J A Gilbert
- Argonne National Laboratory, Institute of Genomic and Systems Biology9700 South Cass Avenue, Argonne, IL, 60439, USA
- Department of Ecology and Evolution, University of Chicago5640 South Ellis Avenue, Chicago, IL, 60637, USA
| | - A M Osborn
- Department of Animal and Plant Sciences, University of SheffieldSheffield, S10 2TN, UK
- Department of Biological Sciences, University of HullHull, HU6 7RX, UK
- School of Life Sciences, University of Lincoln, Brayford PoolLincoln, LN6 7TS, UK
| | - S Widdicombe
- Plymouth Marine LaboratoryProspect Place, Plymouth, PL1 3DH, UK
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62
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Brugère JF, Mihajlovski A, Missaoui M, Peyret P. Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics. Expert Rev Mol Diagn 2014; 9:353-65. [DOI: 10.1586/erm.09.16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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63
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Zhang ZQ, He C, Li ML. Analysis of intestinal bacterial community diversity of adult Dastarcus helophoroides. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:114. [PMID: 25200108 PMCID: PMC4212848 DOI: 10.1093/jis/14.1.114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 02/20/2013] [Indexed: 05/31/2023]
Abstract
Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), and a culturedependent technique were used to study the diversity of the intestinal bacterial community in adult Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae). Universal bacterial primers targeting 200 bp regions of the 16S rDNA gene were used in the PCR-DGGE assay, and 14 bright bands were obtained. The intestinal bacteria detected by PCR-DGGE were classified to Enterococcus (Lactobacillales: Enterococcaceae), Bacillus (Bacillales: Bacillaceae), Cellvibrio (Pseudomonadales: Pseudomonadaceae), Caulobacter (Caulobacterales: Caulobacteraceae), and uncultured bacteria, whereas those isolated by the culture-dependent technique belonged to Staphylococcus (Bacillales: Staphylococcaceae), Pectobacterium Enterobacteriales: Enterobacteriaceae), and Enterobacter (Enterobacteriales: Enterobacteriaceae). These intestinal bacteria represented the groups Lactobacillales (Enterococcus), Pseudomonadales (Cellvibrio), Caulobacterales (Caulobacter), Bacilli (Bacillus and Staphylococcus), and Gammaproteobacteria (Pectobacterium and Enterobacter). Our results demonstrated that PCR-DGGE analysis and the culture-dependent technique were useful in determining the intestinal bacteria of D. helophoroides and the two methods should be integrated to characterize the microbial community and diversity.
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Affiliation(s)
- Z. Q. Zhang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - C. He
- Wuwei academy of Forestry Sciences, WuWei, Gansu, 733000, China
| | - M. L. Li
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
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64
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Angly FE, Dennis PG, Skarshewski A, Vanwonterghem I, Hugenholtz P, Tyson GW. CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. MICROBIOME 2014; 2:11. [PMID: 24708850 PMCID: PMC4021573 DOI: 10.1186/2049-2618-2-11] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/17/2014] [Indexed: 05/13/2023]
Abstract
BACKGROUND Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species. RESULTS Based on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GCN) is strongly linked to microbial phylogenetic taxonomy, potentially under-representing Archaea in amplicon microbial profiles. Using this relationship, we inferred the GCN of all bacterial and archaeal lineages in the Greengenes database within a phylogenetic framework. We created CopyRighter, new software which uses these estimates to correct 16S rRNA amplicon microbial profiles and associated quantitative (q)PCR total abundance. CopyRighter parses microbial profiles and, because GCN estimates are pre-computed for all taxa in the reference taxonomy, rapidly corrects GCN bias. Software validation with in silico and in vitro mock communities indicated that GCN correction results in more accurate estimates of microbial relative abundance and improves the agreement between metagenomic and amplicon profiles. Analyses of human-associated and anaerobic digester microbiomes illustrate that correction makes tangible changes to estimates of qPCR total abundance, α and β diversity, and can significantly change biological interpretation. For example, human gut microbiomes from twins were reclassified into three rather than two enterotypes after GCN correction. CONCLUSIONS The CopyRighter bioinformatic tools permits rapid correction of GCN in microbial surveys, resulting in improved estimates of microbial abundance, α and β diversity.
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Affiliation(s)
- Florent E Angly
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Paul G Dennis
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Current affiliation: School of Agriculture and Food Sciences, Level 3, Hartley Teakle Building (83), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Adam Skarshewski
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Advanced Water Management Center, Level 4, Gehrmann Laboratories Building (60), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Advanced Water Management Center, Level 4, Gehrmann Laboratories Building (60), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
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65
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Sharma B, Narzary D, Jha DK. Culture Independent Diversity Analysis of Soil Microbial Community and their Significance. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2014. [DOI: 10.1007/978-3-319-05936-5_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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66
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Zhang ZQ, He C, Li ML. Analysis of intestinal bacterial community diversity of adult Dastarcus helophoroides. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:114. [PMID: 25200108 PMCID: PMC4212848 DOI: 10.1673/031.014.114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 02/20/2013] [Indexed: 06/03/2023]
Abstract
Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), and a culturedependent technique were used to study the diversity of the intestinal bacterial community in adult Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae). Universal bacterial primers targeting 200 bp regions of the 16S rDNA gene were used in the PCR-DGGE assay, and 14 bright bands were obtained. The intestinal bacteria detected by PCR-DGGE were classified to Enterococcus (Lactobacillales: Enterococcaceae), Bacillus (Bacillales: Bacillaceae), Cellvibrio (Pseudomonadales: Pseudomonadaceae), Caulobacter (Caulobacterales: Caulobacteraceae), and uncultured bacteria, whereas those isolated by the culture-dependent technique belonged to Staphylococcus (Bacillales: Staphylococcaceae), Pectobacterium Enterobacteriales: Enterobacteriaceae), and Enterobacter (Enterobacteriales: Enterobacteriaceae). These intestinal bacteria represented the groups Lactobacillales (Enterococcus), Pseudomonadales (Cellvibrio), Caulobacterales (Caulobacter), Bacilli (Bacillus and Staphylococcus), and Gammaproteobacteria (Pectobacterium and Enterobacter). Our results demonstrated that PCR-DGGE analysis and the culture-dependent technique were useful in determining the intestinal bacteria of D. helophoroides and the two methods should be integrated to characterize the microbial community and diversity.
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Affiliation(s)
- Z. Q. Zhang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - C. He
- Wuwei academy of Forestry Sciences, WuWei, Gansu, 733000, China
| | - M. L. Li
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
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67
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Hyman RW, Fukushima M, Jiang H, Fung E, Rand L, Johnson B, Vo KC, Caughey AB, Hilton JF, Davis RW, Giudice LC. Diversity of the vaginal microbiome correlates with preterm birth. Reprod Sci 2014; 21:32-40. [PMID: 23715799 PMCID: PMC3857766 DOI: 10.1177/1933719113488838] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- Richard W. Hyman
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marilyn Fukushima
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Eula Fung
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Larry Rand
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, CA, USA
| | - Brittni Johnson
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, CA, USA
| | - Kim Chi Vo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, CA, USA
| | - Aaron B. Caughey
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Joan F. Hilton
- Department of Epidemiology and Biostatistics, University of California San Francisco, CA, USA
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Linda C. Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, CA, USA
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68
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Niu SQ, Fukushima J, Jiang Y, Ishikawa Y, Ueda T, Matsumoto S. Analysis of Bacterial Community Structure in the Natural Circulation System Wastewater Bioreactor by Using a 16S rRNA Gene Clone Library. Microbiol Immunol 2013; 50:937-50. [PMID: 17179661 DOI: 10.1111/j.1348-0421.2006.tb03870.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A variety of physical and chemical parameters are routinely monitored during operation of the Natural Circulation System, a wastewater purification bioreactor in which only natural materials and no synthetic chemicals are used. However, the microbial community structures existing in the Natural Circulation System have not been well characterized. Thus, bacterial community structure and composition in this system were studied using clone library analysis of 16S ribosomal RNA genes amplified using PCR with universal bacterial primer sets. The PCR products were then subcloned into the pGEM-T vector. Each unique restriction fragment length polymorphism pattern, created by using two pairs of restriction endonucleases, was designated as an operational taxonomic unit (OTU). The Natural Circulation System comprises five tanks, the second and third of which play a major role in the bioreactor. Clone library pro-files and principal component analysis revealed differences in the bacterial community structures of the second (anaerobic chamber) and the third (aerobic chamber) tanks. However, the beta-proteobacteria, Bacteroidetes/ Chlorobi and gamma-proteobacteria groups were dominant in both tanks. Bacterial composition was more complex in the second tank (107 OTUs) than in the third tank (68 OTUs). Of a total of 154 OTUs in the clone libraries, only 21 were common to the two tanks. The results obtained in this study should provide important information for future research into and management of the Natural Circulation System wastewater bioreactor.
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Affiliation(s)
- Shi-Quan Niu
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Akita, Japan
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69
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Pester M, Maixner F, Berry D, Rattei T, Koch H, Lücker S, Nowka B, Richter A, Spieck E, Lebedeva E, Loy A, Wagner M, Daims H. NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira. Environ Microbiol 2013; 16:3055-71. [PMID: 24118804 DOI: 10.1111/1462-2920.12300] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/26/2013] [Indexed: 12/01/2022]
Abstract
Nitrospira are the most widespread and diverse known nitrite-oxidizing bacteria and key nitrifiers in natural and engineered ecosystems. Nevertheless, their ecophysiology and environmental distribution are understudied because of the recalcitrance of Nitrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of Nitrospira in the environment. Here we introduce nxrB, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for Nitrospira. Phylogenetic trees based on nxrB of Nitrospira were largely congruent to 16S ribosomal RNA-based phylogenies. By using new nxrB-selective polymerase chain reaction primers, we obtained almost full-length nxrB sequences from Nitrospira cultures, two activated sludge samples, and several geographically and climatically distinct soils. Amplicon pyrosequencing of nxrB fragments from 16 soils revealed a previously unrecognized diversity of terrestrial Nitrospira with 1801 detected species-level operational taxonomic units (OTUs) (using an inferred species threshold of 95% nxrB identity). Richness estimates ranged from 10 to 946 coexisting Nitrospira species per soil. Comparison with an archaeal amoA dataset obtained from the same soils [Environ. Microbiol. 14: 525-539 (2012)] uncovered that ammonia-oxidizing archaea and Nitrospira communities were highly correlated across the soil samples, possibly indicating shared habitat preferences or specific biological interactions among members of these nitrifier groups.
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Affiliation(s)
- Michael Pester
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Ecology Centre, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
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70
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Balashov SV, Mordechai E, Adelson ME, Gygax SE. Identification, quantification and subtyping of Gardnerella vaginalis in noncultured clinical vaginal samples by quantitative PCR. J Med Microbiol 2013; 63:162-175. [PMID: 24200640 DOI: 10.1099/jmm.0.066407-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gardnerella vaginalis is an important component of the human vaginal microflora. It is proposed to play a key role in the pathogenesis of bacterial vaginosis (BV), the most common vaginal condition. Here we describe the development, validation and comparative analysis of a novel molecular approach capable of G. vaginalis identification, quantification and subtyping in noncultured vaginal specimens. Using two quantitative PCR (qPCR) assays, we analysed G. vaginalis bacterial loads and clade distribution in 60 clinical vaginal-swab samples. A very high pathogen prevalence was revealed by species-specific qPCR not only among BV patients (100 %), but also in healthy women (97 %), although the G. vaginalis concentration was significantly lower in non-BV samples. G. vaginalis clades identified in vaginal specimens by subtyping multiplex qPCR, which targets four clade-specific genetic markers, had frequencies of 53 % for clade 1, 25 % for clade 2, 32 % for clade 3 and 83 % for clade 4. Multiple clades were found in 70 % of samples. Single G. vaginalis clades were represented by clade 1 and clade 4 in 28 % of specimens. A positive association with BV was shown for clade 1 and clade 3, while clade 2 was positively associated with intermediate vaginal microflora, but not with BV. Clade 4 demonstrated no correlation with the disorder. The presence of multiple clades had a high positive association with BV, whereas G. vaginalis identified as a single clade was negatively linked with the condition. Polyclonal G. vaginalis infection may be a risk factor for BV.
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Affiliation(s)
- Sergey V Balashov
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
| | - Eli Mordechai
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
| | - Martin E Adelson
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
| | - Scott E Gygax
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
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71
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Vishnivetskaya TA, Layton AC, Lau MCY, Chauhan A, Cheng KR, Meyers AJ, Murphy JR, Rogers AW, Saarunya GS, Williams DE, Pfiffner SM, Biggerstaff JP, Stackhouse BT, Phelps TJ, Whyte L, Sayler GS, Onstott TC. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol Ecol 2013; 87:217-30. [PMID: 24102625 DOI: 10.1111/1574-6941.12219] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/30/2022] Open
Abstract
The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed β- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.
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72
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Piterina AV, Pembroke JT. Use of PCR-DGGE Based Molecular Methods to Analyse Microbial Community Diversity and Stability during the Thermophilic Stages of an ATAD Wastewater Sludge Treatment Process as an Aid to Performance Monitoring. ISRN BIOTECHNOLOGY 2013; 2013:162645. [PMID: 25937969 PMCID: PMC4393042 DOI: 10.5402/2013/162645] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 08/20/2013] [Indexed: 01/07/2023]
Abstract
PCR and PCR-DGGE techniques have been evaluated to monitor biodiversity indexes within an ATAD (autothermal thermophilic aerobic digestion) system treating domestic sludge for land spread, by examining microbial dynamics in response to elevated temperatures during treatment. The ATAD process utilises a thermophilic population to generate heat and operates at elevated pH due to degradation of sludge solids, thus allowing pasteurisation and stabilisation of the sludge. Genera-specific PCR revealed that Archaea, Eukarya and Fungi decline when the temperature reaches 59°C, while the bacterial lineage constitutes the dominant group at this stage. The bacterial community at the thermophilic stage, its similarity index to the feed material, and the species richness present were evaluated by PCR-DGGE. Parameters such as choice of molecular target (16S rDNA or rpoB genes), and electrophoresis condition, were optimised to maximise the resolution of the method for ATAD. Dynamic analysis of microbial communities was best observed utilising PCR-DGGE analysis of the V6-V8 region of 16S rDNA, while rpoB gene profiles were less informative. Unique thermophilic communities were shown to quickly adapt to process changes, and shown to be quite stable during the process. Such techniques may be used as a monitoring technique for process health and efficiency.
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Affiliation(s)
- Anna V Piterina
- Department of Chemical and Environmental Sciences and the Material and Surface Science Institute (MSSI), University of Limerick, Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical and Environmental Sciences and the Material and Surface Science Institute (MSSI), University of Limerick, Limerick, Ireland
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73
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Nathani NM, Patel AK, Dhamannapatil PS, Kothari RK, Singh KM, Joshi CG. Comparative evaluation of rumen metagenome community using qPCR and MG-RAST. AMB Express 2013; 3:55. [PMID: 24025701 PMCID: PMC3851495 DOI: 10.1186/2191-0855-3-55] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/10/2013] [Indexed: 11/10/2022] Open
Abstract
Microbial profiling of metagenome communities have been studied extensively using MG-RAST and other related metagenome annotation databases. Although, database based taxonomic profiling provides snapshots of the metagenome architecture, their reliability needs to be validated through more accurate methods. Here, we performed qPCR based absolute quantitation of selected rumen microbes in the liquid and solid fraction of the rumen fluid of river buffalo adapted to varying proportion of concentrate to green or dry roughages and compared with the MG-RAST based annotation of the metagenomes sequences of 16S r-DNA amplicons and high throughput shotgun sequencing. Animals were adapted to roughage-to-concentrate ratio in the proportion of 50:50, 75:25 and 100:00, respectively for six weeks. At the end of each treatment, rumen fluid was collected at 3 h post feeding. qPCR revealed that the relative abundance of Prevotella bryantii was higher, followed by the two cellulolytic bacteria Fibrobacter succinogens and Ruminococcus flavefaciens that accounted up to 1.33% and 0.78% of the total rumen bacteria, respectively. While, Selenomonas ruminantium and archaea Methanomicrobiales were lower in microbial population in the rumen of buffalo. There was no statistically significant difference between the enumerations shown by qPCR and analysis of the shotgun sequencing data by MG-RAST except for Prevotella. These results indicate the variations in abundance of different microbial species in buffalo rumen under varied feeding regimes as well as in different fractions of rumen liquor, i.e. solid and the liquid. The results also present the reliability of shotgun sequencing to describe metagenome and analysis/annotation by MG-RAST.
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74
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Zhang Y, Hunt HK, Hu Z. Application of bacteriophages to selectively remove Pseudomonas aeruginosa in water and wastewater filtration systems. WATER RESEARCH 2013; 47:4507-4518. [PMID: 23764600 DOI: 10.1016/j.watres.2013.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 06/02/2023]
Abstract
Water and wastewater filtration systems often house pathogenic bacteria, which must be removed to ensure clean, safe water. Here, we determine the persistence of the model bacterium Pseudomonas aeruginosa in two types of filtration systems, and use P. aeruginosa bacteriophages to determine their ability to selectively remove P. aeruginosa. These systems used beds of either anthracite or granular activated carbon (GAC), which were operated at an empty bed contact time (EBCT) of 45 min. The clean bed filtration systems were loaded with an instantaneous dose of P. aeruginosa at a total cell number of 2.3 (± 0.1 [standard deviation]) × 10(7) cells. An immediate dose of P. aeruginosa phages (1 mL of phage stock at the concentration of 2.7 × 10(7) PFU (Plaque Forming Units)/mL) resulted in a reduction of 50% (± 9%) and >99.9% in the effluent P. aeruginosa concentrations in the clean anthracite and GAC filters, respectively. To further evaluate the effects of P. aeruginosa phages, synthetic stormwater was run through anthracite and GAC biofilters where mixed-culture biofilms were present. Eighty five days after an instantaneous dose of P. aeruginosa (2.3 × 10(7) cells per filter) on day 1, 7.5 (± 2.8) × 10(7) and 1.1 (± 0.5) × 10(7) P. aeruginosa cells/g filter media were detected in the top layer (close to the influent port) of the anthracite and GAC biofilters, respectively, demonstrating the growth and persistence of pathogenic bacteria in the biofilters. A subsequent 1-h dose of phages, at the concentration of 5.1 × 10(6) PFU/mL and flow rate of 1.6 mL/min, removed the P. aeruginosa inside the GAC biofilters and the anthracite biofilters by 70% (± 5%) and 56% (± 1%), respectively, with no P. aeruginosa detected in the effluent, while not affecting ammonia oxidation or the ammonia-oxidizing bacterial community inside the biofilters. These results suggest that phage treatment can selectively remove pathogenic bacteria with minimal impact on beneficial organisms from attached growth systems for effluent quality improvement.
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Affiliation(s)
- Yanyan Zhang
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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75
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Watanarojanaporn N, Longtonglang A, Boonkerd N, Tittabutr P, Lee J, Teaumroong N. Biases for detecting arbuscular mycorrhizal fungal mixture by terminal restriction fragment length polymorphism (T-RFLP). World J Microbiol Biotechnol 2013; 30:77-86. [DOI: 10.1007/s11274-013-1423-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/28/2013] [Indexed: 11/28/2022]
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76
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Gmiterek A, Wójtowicz H, Mackiewicz P, Radwan-Oczko M, Kantorowicz M, Chomyszyn-Gajewska M, Frąszczak M, Bielecki M, Olczak M, Olczak T. The unique hmuY gene sequence as a specific marker of Porphyromonas gingivalis. PLoS One 2013; 8:e67719. [PMID: 23844074 PMCID: PMC3699645 DOI: 10.1371/journal.pone.0067719] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/21/2013] [Indexed: 12/23/2022] Open
Abstract
Porphyromonas gingivalis, a major etiological agent of chronic periodontitis, acquires heme from host hemoproteins using the HmuY hemophore. The aim of this study was to develop a specific P. gingivalis marker based on a hmuY gene sequence. Subgingival samples were collected from 66 patients with chronic periodontitis and 40 healthy subjects and the entire hmuY gene was analyzed in positive samples. Phylogenetic analyses demonstrated that both the amino acid sequence of the HmuY protein and the nucleotide sequence of the hmuY gene are unique among P. gingivalis strains/isolates and show low identity to sequences found in other species (below 50 and 56%, respectively). In agreement with these findings, a set of hmuY gene-based primers and standard/real-time PCR with SYBR Green chemistry allowed us to specifically detect P. gingivalis in patients with chronic periodontitis (77.3%) and healthy subjects (20%), the latter possessing lower number of P. gingivalis cells and total bacterial cells. Isolates from healthy subjects possess the hmuY gene-based nucleotide sequence pattern occurring in W83/W50/A7436 (n = 4), 381/ATCC 33277 (n = 3) or TDC60 (n = 1) strains, whereas those from patients typically have TDC60 (n = 21), W83/W50/A7436 (n = 17) and 381/ATCC 33277 (n = 13) strains. We observed a significant correlation between periodontal index of risk of infectiousness (PIRI) and the presence/absence of P. gingivalis (regardless of the hmuY gene-based sequence pattern of the isolate identified [r = 0.43; P = 0.0002] and considering particular isolate pattern [r = 0.38; P = 0.0012]). In conclusion, we demonstrated that the hmuY gene sequence or its fragments may be used as one of the molecular markers of P. gingivalis.
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Affiliation(s)
- Anna Gmiterek
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Halina Wójtowicz
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Małgorzata Radwan-Oczko
- Department of Periodontology, Unit of Oral Pathology, Wrocław Medical University, Wrocław, Poland
| | - Małgorzata Kantorowicz
- Department of Periodontology and Oral Medicine, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Maria Chomyszyn-Gajewska
- Department of Periodontology and Oral Medicine, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Magdalena Frąszczak
- Institute of Genetics, University of Environmental and Life Sciences, Wrocław, Poland
| | - Marcin Bielecki
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Teresa Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- * E-mail:
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77
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Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates. Protist 2013; 164:369-79. [DOI: 10.1016/j.protis.2012.11.006] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 10/31/2012] [Accepted: 11/30/2012] [Indexed: 11/13/2022]
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78
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Novel stem–loop probe DNA arrays: Detection of specific acetotrophic 16S ribosomal RNA signatures. Anal Biochem 2013; 435:60-7. [DOI: 10.1016/j.ab.2012.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 11/24/2012] [Accepted: 12/03/2012] [Indexed: 11/19/2022]
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79
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80
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Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 2013; 8:e57923. [PMID: 23460914 PMCID: PMC3583900 DOI: 10.1371/journal.pone.0057923] [Citation(s) in RCA: 640] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/28/2013] [Indexed: 11/19/2022] Open
Abstract
16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacterial genomes to explore the variability of 16S rRNA sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome and DNA abundances. In total, 7,081 16S rRNA sequences were in silico extracted from 1,690 available bacterial genomes (1-15 per genome). While there are several phyla containing low 16S rRNA copy numbers, in certain taxa, e.g., the Firmicutes and Gammaproteobacteria, the variation is large. Genome sizes are more conserved at all tested taxonomic levels than 16S rRNA copy numbers. Only a minority of bacterial genomes harbors identical 16S rRNA gene copies, and sequence diversity increases with increasing copy numbers. While certain taxa harbor dissimilar 16S rRNA genes, others contain sequences common to multiple species. Sequence identity clusters (often termed operational taxonomic units) thus provide an imperfect representation of bacterial taxa of a certain phylogenetic rank. We have demonstrated that the information on 16S rRNA copy numbers and genome sizes of genome-sequenced bacteria may be used as an estimate for the closest related taxon in an environmental dataset to calculate alternative estimates of the relative abundance of individual bacterial taxa in environmental samples. Using an example from forest soil, this procedure would increase the abundance estimates of Acidobacteria and decrease these of Firmicutes. Using the currently available information, alternative estimates of bacterial community composition may be obtained in this way if the variation of 16S rRNA copy numbers among bacteria is considered.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Praha, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Praha, Czech Republic
- * E-mail:
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81
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Can abundance of protists be inferred from sequence data: a case study of foraminifera. PLoS One 2013; 8:e56739. [PMID: 23431390 PMCID: PMC3576339 DOI: 10.1371/journal.pone.0056739] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/14/2013] [Indexed: 12/03/2022] Open
Abstract
Protists are key players in microbial communities, yet our understanding of their role in ecosystem functioning is seriously impeded by difficulties in identification of protistan species and their quantification. Current microscopy-based methods used for determining the abundance of protists are tedious and often show a low taxonomic resolution. Recent development of next-generation sequencing technologies offered a very powerful tool for studying the richness of protistan communities. Still, the relationship between abundance of species and number of sequences remains subjected to various technical and biological biases. Here, we test the impact of some of these biological biases on sequence abundance of SSU rRNA gene in foraminifera. First, we quantified the rDNA copy number and rRNA expression level of three species of foraminifera by qPCR. Then, we prepared five mock communities with these species, two in equal proportions and three with one species ten times more abundant. The libraries of rDNA and cDNA of the mock communities were constructed, Sanger sequenced and the sequence abundance was calculated. The initial species proportions were compared to the raw sequence proportions as well as to the sequence abundance normalized by rDNA copy number and rRNA expression level per species. Our results showed that without normalization, all sequence data differed significantly from the initial proportions. After normalization, the congruence between the number of sequences and number of specimens was much better. We conclude that without normalization, species abundance determination based on sequence data was not possible because of the effect of biological biases. Nevertheless, by taking into account the variation of rDNA copy number and rRNA expression level we were able to infer species abundance, suggesting that our approach can be successful in controlled conditions.
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82
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Jung JY, Lee SH, Lee HJ, Jeon CO. Microbial succession and metabolite changes during fermentation of saeu-jeot: traditional Korean salted seafood. Food Microbiol 2013; 34:360-8. [PMID: 23541203 DOI: 10.1016/j.fm.2013.01.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 01/02/2013] [Accepted: 01/16/2013] [Indexed: 01/13/2023]
Abstract
Saeu-jeot is made by the fermentation of highly salted [approximately 25% (w/v)] shrimp in Korea. Saeu-jeot samples were prepared in triplicate and their cell number, bacterial community, and metabolites were monitored periodically for 183 days. Quantitative PCR showed that bacterial populations were much more abundant than archaeal populations during the entire saeu-jeot fermentation period, which suggested that bacterial populations, not archaeal populations, might be primarily responsible for saeu-jeot fermentation. Pyrosequencing analysis revealed that Proteobacteria were dramatically replaced with halophilic Firmicutes as the fermentation progressed and members of Pseudoalteromonas, Staphylococcus, Salimicrobium, and Alkalibacillus were sequentially dominant and, eventually, Halanaerobium predominated after 66 days of fermentation. Halophilic archaeal genera, Halorubrum, Halolamina, Halobacterium, Haloarcula, and Haloplanus belonging to Euryarchaeota, were dominant, but their communities were relatively constant over the entire fermentation period. Metabolite analysis using a (1)H NMR spectroscopy showed that the amount of metabolites including amino acids, glycerol, and nitrogen compounds rapidly increased during the early fermentation stage, but their levels were relatively constant or they decreased after approximately 49 days of fermentation. A statistical analysis based on bacterial communities and metabolites demonstrated that members of Halanaerobium might be responsible for the production of acetate, butyrate, and methylamines after 66 days of fermentation, which could be considered as a potential indicator to decide the appropriate seafood fermentation time. This study will provide insights into the microbial succession and metabolites of fermented seafood and allow for a greater understanding of the relationships between the microbial community and metabolites in seafood fermentation.
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Affiliation(s)
- Ji Young Jung
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
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83
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Rectal swabs are suitable for quantifying the carriage load of KPC-producing carbapenem-resistant Enterobacteriaceae. Antimicrob Agents Chemother 2013; 57:1474-9. [PMID: 23295937 DOI: 10.1128/aac.01275-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
It is more convenient and practical to collect rectal swabs than stool specimens to study carriage of colon pathogens. In this study, we examined the ability to use rectal swabs rather than stool specimens to quantify Klebsiella pneumoniae carbapenemase (KPC)-producing carbapenem-resistant Enterobacteriaceae (CRE). We used a quantitative real-time PCR (qPCR) assay to determine the concentration of the bla(KPC) gene relative to the concentration of 16S rRNA genes and a quantitative culture-based method to quantify CRE relative to total aerobic bacteria. Our results demonstrated that rectal swabs are suitable for quantifying the concentration of KPC-producing CRE and that qPCR showed higher correlation between rectal swabs and stool specimens than the culture-based method.
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84
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Miller CS. Assembling full-length rRNA genes from short-read metagenomic sequence datasets using EMIRGE. Methods Enzymol 2013; 531:333-52. [PMID: 24060129 DOI: 10.1016/b978-0-12-407863-5.00017-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Microbial ecologists have reaped enormous benefit from advances in high-throughput DNA sequencing. However, the short read lengths of currently dominant technologies have made a seemingly simple question about shotgun metagenomic experiments difficult to answer: what small subunit ribosomal RNA (SSU rRNA) genes are present in a sequenced biological sample? Without these gene sequences, it is difficult to interpret a sample within the rich context of ribosomal rRNA databases accumulated over decades. This chapter presents specialized software, EMIRGE, for the assembly of SSU rRNA genes. EMIRGE is optimized to deal with strain similarity and the fluctuating levels of conservation within the SSU rRNA gene that make assembly difficult. It has been used to successfully assemble genes from shotgun metagenomes, long PCR amplicons, and total-RNA transcriptomes. A detailed discussion of how EMIRGE works and how it deals with the uncertainty inherent in the assembly problem is presented. Practical suggestions are given for understanding and optimizing parameter choice, data preprocessing and postprocessing, and creation of a candidate SSU rRNA gene database. When high-throughput sequencing data are available, EMIRGE can serve as a valuable tool for interpreting microbial community structure.
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Affiliation(s)
- Christopher S Miller
- Department of Integrative Biology, University of Colorado Denver, Campus Box 171, P.O. Box 173364, Denver, Colorado, USA.
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85
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He C, Nan X, Zhang Z, Li M. Composition and diversity analysis of the gut bacterial community of the Oriental armyworm, Mythimna separata, determined by culture-independent and culture-dependent techniques. JOURNAL OF INSECT SCIENCE (ONLINE) 2013; 13:165. [PMID: 24773514 PMCID: PMC4015408 DOI: 10.1673/031.013.16501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/15/2012] [Indexed: 06/03/2023]
Abstract
The intestinal bacteria community structure and diversity of the Oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae), was studied by analysis of a 16S rDNA clone library, denaturing gradient gel electrophoresis,and culture-dependent techniques. The 16S rDNA clone library revealed a bacterial community diversity comprising Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes and Proteobacteria, among which Escherichia coli (Migula) (Enterobacteriales: Enterobacteriaceae) was the dominant bacteria. The intestinal bacteria isolated by PCR-denaturing gradient gel electrophoresis were classified to Firmicutes, Proteobacteria, and Gracilicutes, and E. coli was again the dominant bacteria. The culture-dependent technique showed that the intestinal bacteria belonged to Firmicutes and Actinobacteria, and Staphylococcus was the dominant bacteria. The intestinal bacteria of M. separata were widely distributed among the groups Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes, Proteobacteria, and Gracilicutes. 16S rDNA clone library, denaturing gradient gel electrophoresis, and culture-dependent techniques should be integrated to obtain precise results in terms of the microbial community and its diversity.
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Affiliation(s)
- Cai He
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
- Wuwei Academy of Forestry Sciences, Wuwei, Gansu, 733000, P.R. China
| | - Xiaoning Nan
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Zhengqing Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Menglou Li
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
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86
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Depletion of unwanted nucleic acid templates by selective cleavage: LNAzymes, catalytically active oligonucleotides containing locked nucleic acids, open a new window for detecting rare microbial community members. Appl Environ Microbiol 2012; 79:1534-44. [PMID: 23263968 DOI: 10.1128/aem.03392-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined with in vitro transcription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer "Candidatus Nitrospira defluvii." In silico analysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition.
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87
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Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol 2012; 8:e1002743. [PMID: 23133348 PMCID: PMC3486904 DOI: 10.1371/journal.pcbi.1002743] [Citation(s) in RCA: 278] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 08/31/2012] [Indexed: 02/01/2023] Open
Abstract
The abundance of different SSU rRNA (“16S”) gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly – from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data. Microbial ecologists cannot observe their study organisms directly, so they use molecular sequencing to measure the abundance of different microbes living in the wild. The most commonly used method for measuring the abundance of different microbes is to collect a DNA sample from an environment and sequence a particular gene, the 16S SSU rRNA gene (“16S”) from those samples. The abundance of 16S sequences from different microbes is then used as a surrogate measure of the abundance of the microbial taxa in the community. One problem with the use of the 16S gene as a measure of microbial abundance is that many microbes have multiple copies of the gene in their genome. Thus, variation in 16S gene abundances can be caused by both genomic copy number variation and variation in the abundance of organisms. In this study we present a computational method that allows estimation of the abundance and genomic 16S copy number of microbes based on environmental sequencing of the 16S gene. We use simulations and analysis of microbial community data sets to demonstrate that estimating the abundance of organisms from 16S data improves our ability to accurately measure the diversity and abundance of microbial communities.
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Affiliation(s)
- Steven W Kembel
- Institute of Ecology & Evolution, University of Oregon, Eugene, Oregon, USA.
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88
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Moffett BF, Nicholson FA, Uwakwe NC, Chambers BJ, Harris JA, Hill TCJ. Zinc contamination decreases the bacterial diversity of agricultural soil. FEMS Microbiol Ecol 2012; 43:13-9. [PMID: 19719692 DOI: 10.1111/j.1574-6941.2003.tb01041.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Abstract Around half a million tonnes of biosolids (sewage sludge dry solids) are applied to agricultural land in the United Kingdom each year, and this may increase to 732 000 t by 2005/6. The heavy metals contained in biosolids may permanently degrade the microbial decomposer communities of agricultural soils. We used amplified ribosomal DNA restriction analysis of the extractable bacterial fraction to compare the diversity of a zinc-contaminated soil (400 mg kg(-1) Zn; pH 5.7 and 1.36% C(org)) with that of a control soil (57 mg kg(-1) Zn; pH 6.2 and 1.40% C(org)) from a long-term sewage sludge experiment established in 1982 at ADAS Gleadthorpe. Comparison of the restriction fragment length polymorphisms of 236 clones from each soil suggested that the stress caused by zinc toxicity had lowered bacterial diversity. There were 120 operational taxonomic units (OTUs) in the control soil, but only 90 in the treated soil, a decrease of 25%. While the control soil had 82 single-occurrence OTUs the contaminated soil had only 52. The fall in diversity was accompanied by a decrease in evenness. The most abundant OTUs in the contaminated soil (which tended to be common to both soils) accounted for a higher proportion of clones than in the control. The most dominant OTU, in both soils, belonged to the Rubrobacter radiotolerans group of the high G+C Gram-positive bacteria. The data was also used to develop efficient sampling strategies.
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Affiliation(s)
- Bruce F Moffett
- School of Health and Bioscience, University of East London, Romford Rd., Stratford, London E15 4LZ, UK
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89
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Pearce DA, Gast CJ, Lawley B, Ellis-Evans JC. Bacterioplankton community diversity in a maritime Antarctic lake, determined by culture-dependent and culture-independent techniques. FEMS Microbiol Ecol 2012; 45:59-70. [PMID: 19719607 DOI: 10.1016/s0168-6496(03)00110-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Abstract The biodiversity of the pelagic bacterioplankton community of a maritime Antarctic freshwater lake was examined by cultivation-dependent and cultivation-independent techniques to determine predominant bacterioplankton populations present. The culture-dependent techniques used were direct culture and observation, polymerase chain reaction amplification of 16S rRNA gene fragments, restriction fragment length polymorphism (RFLP) analysis followed by selective sequencing and fatty acid methyl ester analysis. The culture-independent techniques used were 16S ribosomal DNA gene cloning, RFLP analysis and sequencing, in situ hybridisation with group-specific, fluorescently labelled oligonucleotide probes and cloning and sequencing of dominant denaturing gradient gel electrophoresis products. Significant differences occurred between the results obtained with each method. However, sufficient overlap existed between the different methods to identify potentially significant groups. At least six different bacterial divisions including 24 genera were identified using culture-dependent techniques, and eight different bacterial divisions, including 23 genera, were identified using culture-independent techniques. Only five genera, Corynebacterium, Cytophaga, Flavobacterium, Janthinobacterium and Pseudomonas, could be identified using both sets of techniques, which represented four different bacterial divisions. Significantly for Antarctic freshwater lakes, pigment production is found within members of each of these genera. This work illustrates the importance of a comprehensive polyphasic approach in the analysis of lake bacterioplankton, and supports the ecological relevance of results obtained in earlier entirely culture-based studies.
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Affiliation(s)
- D A Pearce
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
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90
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Ruegger PM, Bent E, Li W, Jeske DR, Cui X, Braun J, Jiang T, Borneman J. Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology. J Microbiol Methods 2012; 90:235-40. [PMID: 22640891 PMCID: PMC3404216 DOI: 10.1016/j.mimet.2012.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/20/2012] [Accepted: 05/20/2012] [Indexed: 10/28/2022]
Abstract
Improvements to oligonucleotide fingerprinting of rRNA genes (OFRG) were obtained by implementing polony microarray technology. OFRG is an array-based method for analyzing microbial community composition. Polonies are discrete clusters of DNA, produced by solid-phase PCR in hydrogels, and derived from individual, spatially isolated DNA molecules. The advantages of a polony-based OFRG method include higher throughput and reductions in the PCR-induced errors and compositional skew inherent in all other PCR-based community composition methods, including high-throughput sequencing of rRNA genes. Given the similarities between polony microarrays and certain aspects of sequencing methods such as the Illumina platform, we suggest that if concepts presented in this study were implemented in high-throughput sequencing protocols, a reduction of PCR-induced errors and compositional skew may be realized.
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Affiliation(s)
- Paul M. Ruegger
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - Elizabeth Bent
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - Wei Li
- Department of Computer Science, University of California, Riverside, CA, USA
| | - Daniel R. Jeske
- Department of Statistics, University of California, Riverside, CA, USA
| | - Xinping Cui
- Department of Statistics, University of California, Riverside, CA, USA
| | - Jonathan Braun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
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91
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Ince O, Basaka B, Inceb BK, Cetecioglua Z, Celikkolb S, Kolukirik M. Effect of nitrogen deficiency during SBR operation on PHA storage and microbial diversity. ENVIRONMENTAL TECHNOLOGY 2012; 33:1827-1837. [PMID: 23240176 DOI: 10.1080/09593330.2011.634441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this study, changes in microbial diversity and polyhydroxyalkanoate storage ability of activated sludge under aerobic dynamic feeding conditions were investigated. Two sequencing batch reactors were operated with and without nitrogen limitation, by applying a moderate sludge retention time. Polymer storage abilities of the biomasses were improved significantly under dynamic conditions, in terms of specific polymer storage rate, polymer storage yield and polymer content of activated sludge. Moreover, aerobic dynamic feeding conditions together with nutrient limitation further improved the storage ability of the mixed population. Polymer storage yields of the biomass enriched under nitrogen-sufficient and nitrogen-deficient conditions were 0.43 and 0.61 Cmmol PHA/Cmmol substrate, respectively. This study also contributes to the knowledge of activated sludge microbiology, providing detailed information about temporal changes in community structure under dynamic conditions. Microbial community structure was determined by 16S rDNA clone library construction. Also changes in communities under different operating conditions were monitored by DGGE analysis based on bacterial 16S rDNA. The beta subclass of Proteobacteria was the most abundant phylum in both reactors during the operation periods. Changes in the community structure occurred in terms of relative abundance of the operational taxonomic units (OTUs) rather than the OTU types present in the system.
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Affiliation(s)
- Orhan Ince
- Department of Environmental Engineering, Istanbul Technical University, 34469, Istanbul, Turkey.
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92
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Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One 2012. [PMID: 22457796 DOI: 10.1371/joumal.pone.0033865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled. METHODOLOGY/PRINCIPAL FINDINGS In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used. CONCLUSIONS/SIGNIFICANCE Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.
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Affiliation(s)
- Sanqing Yuan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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93
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Devine SP, Pelletreau KN, Rumpho ME. 16S rDNA-based metagenomic analysis of bacterial diversity associated with two populations of the kleptoplastic sea slug Elysia chlorotica and its algal prey Vaucheria litorea. THE BIOLOGICAL BULLETIN 2012; 223:138-154. [PMID: 22983039 DOI: 10.1086/bblv223n1p138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The molluscan sea slug Elysia chlorotica is best known for its obligate endosymbiosis with chloroplasts (= kleptoplasty) from its algal prey Vaucheria litorea and its ability to sustain itself photoautotrophically for several months. This unusual photosynthetic sea slug also harbors an array of undescribed bacteria, which may contribute to the long-term success of the symbiosis. Here, we utilized 16S rDNA-based metagenomic analyses to characterize the microbial diversity associated with two populations of E. chlorotica from Halifax, Nova Scotia, Canada, and from Martha's Vineyard, Massachusetts, USA. Animals were examined immediately after collection from their native environments, after being starved of their algal prey for several months, and after being bred in the laboratory (second-generation sea slugs) to characterize the effect of varying environmental and culturing conditions on the associated bacteria. Additionally, the microbiome of the algal prey, laboratory-cultured V. litorea, was analyzed to determine whether the laboratory-bred sea slugs obtained bacteria from their algal food source during development. Bacterial profiles varied between populations and among all conditions except for the F2 laboratory-bred samples, which were similar in diversity and abundance, but not to the algal microbiome. Alpha-, beta-, and gamma-proteobacteria dominated all of the samples along with Actinobacteria, Bacilli, Flavobacteria, and Sphingobacteria. Bacteria capable of polysaccharide digestion and photosynthesis, as well as putative nitrogen fixation, vitamin B(12) production, and natural product biosynthesis were associated with the sea slug and algal samples.
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Affiliation(s)
- Susan P Devine
- University of Maine, Department of Molecular and Biomedical Sciences, Orono, Maine 04469, USA
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94
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Nair A, Gopalan SV, George S, Kumar KS, Merilä J. Cross-species testing and utility of microsatellite loci in Indirana frogs. BMC Res Notes 2012; 5:389. [PMID: 22838958 PMCID: PMC3441609 DOI: 10.1186/1756-0500-5-389] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellite loci are widely used in population and conservation genetic studies of amphibians, but the availability of such markers for tropical and subtropical taxa is currently very limited. In order to develop resources for conservation genetic studies in the genus Indirana, we tested amplification success and polymorphism in 62 previously developed microsatellite loci, in eight Indirana species - including new candidate species. Developing genomic resources for this amphibian taxon is particularly important as it is endemic to the Western Ghats biodiversity hotspot, and harbours several endangered species. FINDINGS The cross-species amplification success rate varied from 11.3 % to 29.0 % depending on the species, with 29 - 80 % of the amplifying loci being polymorphic. A strong negative correlation between cross-species amplification success (and polymorphism) and genetic distance separating target from source species was observed. CONCLUSIONS Our results provide additional genetic support for the existence of genetically divergent cryptic species within the genus Indirana. The tested markers should be useful for population and conservation genetic studies in this genus, and in particular, for species closely related to the source species, I. beddomii.
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Affiliation(s)
- Abhilash Nair
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, FI-00014, Finland.
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95
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Jin HM, Kim JM, Lee HJ, Madsen EL, Jeon CO. Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:7731-7740. [PMID: 22709320 DOI: 10.1021/es3018545] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Following the 2007 oil spill in South Korean tidal flats, we sought to identify microbial players influencing the environmental fate of released polycyclic aromatic hydrocarbons (PAHs). Two years of monitoring showed that PAH concentrations in sediments declined substantially. Enrichment cultures were established using seawater and modified minimal media containing naphthalene as sole carbon source. The enriched microbial community was characterized by 16S rRNA-based DGGE profiling; sequencing selected bands indicated Alteromonas (among others) were active. Alteromonas sp. SN2 was isolated and was able to degrade naphthalene, phenanthrene, anthracene, and pyrene in laboratory-incubated microcosm assays. PCR-based analysis of DNA extracted from the sediments revealed naphthalene dioxygenase (NDO) genes of only two bacterial groups: Alteromonas and Cycloclasticus, having gentisate and catechol metabolic pathways, respectively. However, reverse transcriptase PCR-based analysis of field-fixed mRNA revealed in situ expression of only the Alteromonas-associated NDO genes; in laboratory microcosms these NDO genes were markedly induced by naphthalene addition. Analysis by GC/MS showed that naphthalene in tidal-flat samples was metabolized predominantly via the gentisate pathway; this signature metabolite was detected (0.04 μM) in contaminated field sediment. A quantitative PCR-based two-year data set monitoring Alteromonas-specific 16S rRNA genes and NDO transcripts in sea-tidal flat field samples showed that the abundance of bacteria related to strain SN2 during the winter season was 20-fold higher than in the summer season. Based on the above data, we conclude that strain SN2 and its relatives are site natives--key players in PAH degradation and adapted to winter conditions in these contaminated sea-tidal-flat sediments.
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Affiliation(s)
- Hyun Mi Jin
- School of Biological Sciences, Chung-Ang University , 84, HeukSeok-Ro, Seoul 156-756, Republic of Korea
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96
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Magwira CA, Kullin B, Lewandowski S, Rodgers A, Reid SJ, Abratt VR. Diversity of faecal oxalate-degrading bacteria in black and white South African study groups: insights into understanding the rarity of urolithiasis in the black group. J Appl Microbiol 2012; 113:418-28. [PMID: 22616725 DOI: 10.1111/j.1365-2672.2012.05346.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/02/2012] [Accepted: 05/14/2012] [Indexed: 12/13/2022]
Abstract
AIM To examine whether enhanced diversity or numbers of oxalate-degrading bacteria in the gastrointestinal tracts of black South Africans play a role in determining the rarity of urolithiasis in this group. METHODS AND RESULTS Fresh faecal samples collected from healthy black and white South African male volunteers were analysed in terms of bacterial oxalate-degrading activity, bacterial diversity and relative species abundance. Varied bacterial populations prepared from samples from the low-risk black group showed a significantly higher level of oxalate degradation. Denaturing gradient gel electrophoresis analyses of Lactobacillus and related spp. and Bifidobacterium spp. 16S rRNA PCR products revealed a significantly higher faecal Lactobacillus diversity for the low-risk black group relative to the higher-risk white group. Quantitative real-time PCR experiments did not show any significant differences between the study groups for Lactobacillus and related spp.. However, Bifidobacterium spp. were present at a significantly higher relative abundance in the black group. Oxalobacter formigenes was present only at very low levels in either group. CONCLUSIONS The low abundance of O. formigenes and increased diversity and abundance of oxalate-degrading Lactobacillus and Bifidobacterium spp. in the black South African population suggest that these strains rather than O. formigenes may protect this group against calcium oxalate kidney stone disease. SIGNIFICANCE AND IMPACT OF THE STUDY The South African black population harbours a pool of potential oxalate-degrading lactic acid bacteria, which is more abundant and diverse than that of white South Africans. This may be useful in developing probiotics for calcium oxalate kidney stone prophylaxis.
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Affiliation(s)
- C A Magwira
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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97
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Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and ¹H nuclear magnetic resonance spectroscopy. Appl Environ Microbiol 2012; 78:5983-93. [PMID: 22706048 DOI: 10.1128/aem.00104-12] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pyrosequencing of 16S rRNA genes (targeting Bacteria and Archaea) and (1)H nuclear magnetic resonance were applied to investigate the rumen microbiota and metabolites of Hanwoo steers in the growth stage (HGS), Hanwoo steers in the late fattening stage (HFS), Holstein-Friesian dairy cattle (HDC), and Korean native goats (KNG) in the late fattening stage. This was a two-part investigation. We began by comparing metabolites and microbiota of Hanwoo steers at two stages of husbandry. Statistical comparisons of metabolites and microbial communities showed no significant differences between HFS and HGS (differing by a dietary shift at 24 months and age [67 months versus 12 months]). We then augmented the study by extending the investigation to HDC and KNG. Overall, pyrosequencing of 16S rRNA genes showed that the rumens had highly diverse microbial communities containing many previously undescribed microorganisms. Bioinformatic analysis revealed that the bacterial sequences were predominantly affiliated with four phyla-Bacteroidetes, Firmicutes, Fibrobacteres, and Proteobacteria-in all ruminants. However, interestingly, the bacterial reads belonging to Fibrobacteres were present at a very low abundance (<0.1%) in KNG. Archaeal community analysis showed that almost all of these reads fell into a clade related to, but distinct from, known cultivated methanogens. Statistical analyses showed that the microbial communities and metabolites of KNG were clearly distinct from those of other ruminants. In addition, bacterial communities and metabolite profiles of HGS and HDC, fed similar diets, were distinctive. Our data indicate that bovine host breeds override diet as the key factor that determines bacterial community and metabolite profiles in the rumen.
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98
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Greeff MR, Christison KW, Macey BM. Development and preliminary evaluation of a real-time PCR assay for Halioticida noduliformans in abalone tissues. DISEASES OF AQUATIC ORGANISMS 2012; 99:103-117. [PMID: 22691979 DOI: 10.3354/dao02468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Abalone Haliotis midae exhibiting typical clinical signs of tubercle mycosis were discovered in South African culture facilities in 2006, posing a significant threat to the industry. The fungus responsible for the outbreak was identified as a Peronosporomycete, Halioticida noduliformans. Currently, histopathology and gross observation are used to diagnose this disease, but these 2 methods are neither rapid nor sensitive enough to provide accurate and reliable diagnosis. Real-time quantitative PCR (qPCR) is a rapid and reliable method for the detection and quantification of a variety of pathogens, so therefore we aimed to develop a qPCR assay for species-specific detection and quantification of H. noduliformans. Effective extraction of H. noduliformans genomic DNA from laboratory grown cultures, as well as from spiked abalone tissues, was accomplished by grinding samples using a pellet pestle followed by heat lysis in the presence of Chelax-100 beads. A set of oligonucleotide primers was designed to specifically amplify H. noduliformans DNA in the large subunit (LSU) rRNA gene, and tested for cross-reactivity to DNA extracted from related and non-related fungi isolated from seaweeds, crustaceans and healthy abalone; no cross-amplification was detected. When performing PCR assays in an abalone tissue matrix, an environment designed to be a non-sterile simulation of environmental conditions, no amplification occurred in the negative controls. The qPCR assay sensitivity was determined to be approximately 0.28 pg of fungal DNA (~2.3 spores) in a 25 µl reaction volume. Our qPCR technique will be useful for monitoring and quantifying H. noduliformans for the surveillance and management of abalone tubercle mycosis in South Africa.
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Affiliation(s)
- Mariska R Greeff
- Biodiversity and Conservation Biology, University of Western Cape, Bellville, South Africa
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99
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Isolation, identification and monitoring of contaminant bacteria in Iranian Kefir type drink by 16S rDNA sequencing. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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100
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Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One 2012; 7:e33865. [PMID: 22457796 PMCID: PMC3311548 DOI: 10.1371/journal.pone.0033865] [Citation(s) in RCA: 343] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 02/23/2012] [Indexed: 01/28/2023] Open
Abstract
Background DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled. Methodology/Principal Findings In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used. Conclusions/Significance Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.
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