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Soundharrajan I, Jung JS, Muthusamy K, Lee BH, Park HS, Sivanesan R, Choi KC. Effects of Different Lactic Acid Bacteria in Single or Mixed Form on the Fermentative Parameters and Nutrient Contents of Early Heading Triticale Silage for Livestock. Foods 2023; 12:4296. [PMID: 38231774 DOI: 10.3390/foods12234296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
Lactic acid bacteria (LAB) are excellent anaerobic fermenters that produce highly valuable grass-based animal feed containing essential nutrients. In the present study, an ensiling process was used to improve anaerobic fermentation in triticale silage under different moisture conditions with LAB. The triticale was treated with either a single bacterium or combined LAB and then vacuum-sealed. After 180 and 360 days of storage, the silage's fermentation characteristics, microbial changes and nutrient contents were analyzed. The pH of the silage was significantly lower than the control silage. There was a significant difference in the pH values between the silages treated with single or mixed LAB. The LAB treatment led to a substantial increase in lactic acid (LA), a decrease in butyric acid (BA), and marginal levels of acetic acid (AA). The LA content after the mixed LAB treatment was significantly higher than that after the single culture LAB treatment. After single or combined inoculant treatments, the LAB population in the silage increased, while the yeast and mold levels decreased. These findings suggest that the addition of LAB to silage during ensiling could enhance the nutritional quality and reduce unwanted microbial growth. The mixed LAB treatments produced silage with a significantly higher nutritional value than the single LAB treatments.
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Affiliation(s)
- Ilavenil Soundharrajan
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea
| | - Jeong Sung Jung
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea
| | - Karnan Muthusamy
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea
| | - Bae Hun Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea
| | - Hyung Soo Park
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea
| | - Ravikumar Sivanesan
- Department of Zoology, Rajah Serfoji Government College (Autonomous), Thanjavur 613-005, India
| | - Ki Choon Choi
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea
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2
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Campos MJ, Gallardo A, Quesada A. Optimized Design of Degenerate Primers for PCR Based on DNA or Protein Sequence Comparisons. Methods Mol Biol 2023; 2967:239-251. [PMID: 37608116 DOI: 10.1007/978-1-0716-3358-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
PCR with degenerate primers can be used to identify the coding sequence of an unknown protein or to detect a genetic variant within a gene family. These primers, which are complex mixtures of slightly different oligonucleotide sequences, can be optimized to increase the efficiency and/or specificity of PCR in the amplification of a sequence of interest by the introduction of mismatches with the target sequence and balancing their position toward the primers 5'- or 3'-ends. In this work, we explain in detail examples of rational design of primers in three different applications, including the use of specific determinants at the 3'-end, to (i) improve PCR efficiency with related sequences for members of a protein family by complete degeneration at a core box of conserved genetic information at the 3'-end with the reduction of degeneration at the 5'-end, (ii) optimize specificity of allelic discrimination of closely related DNA sequences of orthologous by 5'-end fully degenerate primers, and (iii) increase the PCR efficiency of primers by targeting DNA sequences belonging to specific phylogenetic groups, within a large and diverse gene family, allowing the use of multiplex/degenerate PCR.
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Affiliation(s)
- Maria Jorge Campos
- MARE-Marine and Environmental Sciences Centre & ARNET-Aquatic Research Network Associated Laboratory, ESTM, Polytechnic of Leiria, Peniche, Portugal.
| | - Alejandro Gallardo
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Alberto Quesada
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
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3
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Heckman TI, Yazdi Z, Pomaranski EK, Sebastião FDA, Mukkatira K, Vuglar BM, Cain KD, Loch TP, Soto E. Atypical flavobacteria recovered from diseased fish in the Western United States. Front Cell Infect Microbiol 2023; 13:1149032. [PMID: 37153143 PMCID: PMC10161732 DOI: 10.3389/fcimb.2023.1149032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/07/2023] [Indexed: 05/09/2023] Open
Abstract
Flavobacterial diseases, caused by bacteria in the order Flavobacteriales, are responsible for devastating losses in farmed and wild fish populations worldwide. The genera Flavobacterium (Family Flavobacteriaceae) and Chryseobacterium (Weeksellaceae) encompass the most well-known agents of fish disease in the order, but the full extent of piscine-pathogenic species within these diverse groups is unresolved, and likely underappreciated. To identify emerging agents of flavobacterial disease in US aquaculture, 183 presumptive Flavobacterium and Chryseobacterium isolates were collected from clinically affected fish representing 19 host types, from across six western states. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis using the gyrB gene. Antimicrobial susceptibility profiles were compared between representatives from each major phylogenetic clade. Of the isolates, 52 were identified as Chryseobacterium species and 131 as Flavobacterium. The majority of Chryseobacterium isolates fell into six clades (A-F) consisting of ≥ 5 fish isolates with ≥ 70% bootstrap support, and Flavobacterium into nine (A-I). Phylogenetic clades showed distinct patterns in antimicrobial susceptibility. Two Chryseobacterium clades (F & G), and four Flavobacterium clades (B, G-I) had comparably high minimal inhibitory concentrations (MICs) for 11/18 antimicrobials tested. Multiple clades in both genera exhibited MICs surpassing the established F. psychrophilum breakpoints for oxytetracycline and florfenicol, indicating potential resistance to two of the three antimicrobials approved for use in finfish aquaculture. Further work to investigate the virulence and antigenic diversity of these genetic groups will improve our understanding of flavobacterial disease, with applications for treatment and vaccination strategies.
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Affiliation(s)
- Taylor I. Heckman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Zeinab Yazdi
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Eric K. Pomaranski
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Fernanda de Alexandre Sebastião
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Fisheries, Embrapa Amazônia Ocidental, Manaus, Amazonas, Brazil
| | - Kaveramma Mukkatira
- Fish Health Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA, United States
| | - Brent M. Vuglar
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, United States
| | - Kenneth D. Cain
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, United States
| | - Thomas P. Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Esteban Soto
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- *Correspondence: Esteban Soto,
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Hisham MB, Hashim AM, Mohd Hanafi N, Abdul Rahman N, Abdul Mutalib NE, Tan CK, Nazli MH, Mohd Yusoff NF. Bacterial communities associated with silage of different forage crops in Malaysian climate analysed using 16S amplicon metagenomics. Sci Rep 2022; 12:7107. [PMID: 35501317 PMCID: PMC9061801 DOI: 10.1038/s41598-022-08819-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Silage produced in tropical countries is prone to spoilage because of high humidity and temperature. Therefore, determining indigenous bacteria as potential inoculants is important to improve silage quality. This study aimed to determine bacterial community and functional changes associated with ensiling using amplicon metagenomics and to predict potential bacterial additives associated with silage quality in the Malaysian climate. Silages of two forage crops (sweet corn and Napier) were prepared, and their fermentation properties and functional bacterial communities were analysed. After ensiling, both silages were predominated by lactic acid bacteria (LAB), and they exhibited good silage quality with significant increment in lactic acid, reductions in pH and water-soluble carbohydrates, low level of acetic acid and the absence of propionic and butyric acid. LAB consortia consisting of homolactic and heterolactic species were proposed to be the potential bacterial additives for sweet corn and Napier silage fermentation. Tax4fun functional prediction revealed metabolic pathways related to fermentation activities (bacterial division, carbohydrate transport and catabolism, and secondary metabolite production) were enriched in ensiled crops (p < 0.05). These results might suggest active transport and metabolism of plant carbohydrates into a usable form to sustain bacterial reproduction during silage fermentation, yielding metabolic products such as lactic acid. This research has provided a comprehensive understanding of bacterial communities before and after ensiling, which can be useful for desirable silage fermentation in Malaysia.
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Affiliation(s)
- Minhalina Badrul Hisham
- Agro-Biotechnology Malaysia Institutes (ABI), National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation (MOSTI), c/o MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Nursyuhaida Mohd Hanafi
- Agro-Biotechnology Malaysia Institutes (ABI), National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation (MOSTI), c/o MARDI Headquarters, 43400, Serdang, Selangor, Malaysia.
| | - Norafizah Abdul Rahman
- Agro-Biotechnology Malaysia Institutes (ABI), National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation (MOSTI), c/o MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Nur Elina Abdul Mutalib
- Institutes for Health Systems Research, National Institutes of Health Malaysia (NIH), 40170, Shah Alam, Selangor, Malaysia
| | - Chun Keat Tan
- Agro-Biotechnology Malaysia Institutes (ABI), National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation (MOSTI), c/o MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Muhamad Hazim Nazli
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Fatihah Mohd Yusoff
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Hagemeijer YP, Guryev V, Horvatovich P. Accurate Prediction of Protein Sequences for Proteogenomics Data Integration. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:233-260. [PMID: 34905178 DOI: 10.1007/978-1-0716-1936-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This book chapter discusses proteogenomics data integration and provides an overview into the different omics layer involved in defining the proteome of a living organism. Various aspects of genome variability affecting either the sequence or abundance level of proteins are discussed in this book chapter, such as the effect of single-nucleotide variants or larger genomic structural variants on the proteome. Next, various sequencing technologies are introduced and discussed from a proteogenomics data integration perspective such as those providing short- and long-read sequencing and listing their respective advantages and shortcomings for accurate protein variant prediction using genomic/transcriptomics sequencing data. Finally, the various bioinformatics tools used to process and analyze DNA/RNA sequencing data are discussed with the ultimate goal of obtaining accurately predicted sample-specific protein sequences that can be used as a drop-in replacement in existing approaches for peptide and protein identification using popular database search engines such as MSFragger, SearchGUI/PeptideShaker.
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Affiliation(s)
- Yanick Paco Hagemeijer
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands.
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6
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Application and Future Prospective of Lactic Acid Bacteria as Natural Additives for Silage Production—A Review. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11178127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ensiling is one of the essential processes to preserve fodder with high nutrients and microbiological quality. The forages before ensiling have a limited number of bacteria associated with the controlled fermentation process. Undesirable microbes can grow in silages when there is not efficient fermentation. Such kinds of microbes might cause pathogenic or toxic compounds that affect animal and human health. Therefore, it is necessary to inoculate potent starter cultures. Lactic acid bacteria’s (LABs) have been considered the most prominent microbial additives used to improve the quality of silage. Currently, LABs have been used in modern and sustainable agriculture systems due to their biological potential. Recently, many scientists have increased their focus on developing nutrient-rich animal feed from forages with LAB. This current review focuses on issues related to forage preservation in the form of silages, how undesirable microbes affect the fermentation process, the critical role of LAB in silage production, and the selection of potent LABs to effectively control unwanted microbial growth and promote those which favor animal growth.
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Pitiwittayakul N, Bureenok S, Schonewille JT. Selective Thermotolerant Lactic Acid Bacteria Isolated From Fermented Juice of Epiphytic Lactic Acid Bacteria and Their Effects on Fermentation Quality of Stylo Silages. Front Microbiol 2021; 12:673946. [PMID: 34381426 PMCID: PMC8350162 DOI: 10.3389/fmicb.2021.673946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/22/2021] [Indexed: 11/21/2022] Open
Abstract
The aim of the present study was to isolate and identify lactic acid bacteria (LAB) from fermented juice of tropical crops such as Napier grass, Ruzi grass, Purple guinea grass, Stylo legume, and Leucaena and their application to improve the quality of tropical crop silage. Fifteen strains of LAB were isolated. The LAB strains were Gram-positive and catalase-negative bacteria and could be divided into three groups, i.e., Pediococcus pentosaceus, Lactiplantibacillus (para)plantarum, and Limosilactobacillus fermentum according to the biochemical API 50CH test. Based on the analysis of 16S rRNA sequence, the strains isolated in the group L. (para)plantarum were distinguished. Two isolates (N3 and G4) were identified as Lactiplantibacillus plantarum. Three isolates (St1, St2, and St3) were identified as L. paraplantarum. In addition, the identification of other isolates was confirmed in the group P. pentosaceus (R1, R4, R5, R8, R11, and L1) and the group L. fermentum (N4, G6, G7, and N4). All selected strains were able to grow at 50°C. All LAB strains showed antimicrobial activity against Escherichia coli ATCC 25922, Shigella sonnei ATCC 25931, Pseudomonas aeruginosa ATCC 27853, and Bacillus cereus ATCC 11778. Four selected LAB strains (St1, St3, N4, and R4) were tested for their capacity to successfully ensile Stylo legume (Stylosanthes guianensis CIAT184). Stylo silages treated with LAB were well preserved, the NH3–N and butyric acid contents were lower, and the lactic acid content was higher than those in the control (p < 0.05). The acetic acid content was the highest in R4-treated silage among the treatments (p < 0.05). The crude protein (CP) content of St1-silage was significantly (p < 0.05) higher than the others. The inoculation of thermotolerant LAB selected from fermented juice of epiphytic lactic acid bacteria (FJLB) was found to be highly instrumental to obtain well-preserved silage from the Stylo legume.
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Affiliation(s)
- Nittaya Pitiwittayakul
- Department of Agricultural Technology and Environment, Rajamangala University of Technology Isan, Nakhon Ratchasima, Thailand
| | - Smerjai Bureenok
- Department of Agricultural Technology and Environment, Rajamangala University of Technology Isan, Nakhon Ratchasima, Thailand
| | - Jan Thomas Schonewille
- Department of Agricultural Technology and Environment, Rajamangala University of Technology Isan, Nakhon Ratchasima, Thailand.,Department of Public Health Sciences, Utrecht University, Utrecht, Netherlands
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8
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Hanafi M, Tahzima R, Ben Kaab S, Tamisier L, Roux N, Massart S. Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection. Pathogens 2020; 9:pathogens9121045. [PMID: 33322809 PMCID: PMC7764570 DOI: 10.3390/pathogens9121045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/05/2023] Open
Abstract
Banana mild mosaic virus (BanMMV) (Betaflexiviridae, Quinvirinae, unassigned species) is a filamentous virus belonging to the Betaflexiviridae family. It infects Musa spp. with a very wide geographic distribution. The genome variability of plant viruses, including the members of the Betaflexiviridae family, makes their molecular detection by specific primers particularly challenging. During routine indexing of the Musa germplasm accessions, a discrepancy was observed between electron microscopy and immunocapture (IC) reverse transcription (RT) polymerase chain reaction (PCR) test results for one asymptomatic accession. Filamentous viral particles were observed while molecular tests failed to amplify any fragment. The accession underwent high-throughput sequencing and two complete genomes of BanMMV with 75.3% of identity were assembled. Based on these sequences and on the 54 coat protein sequences available from GenBank, a new forward primer, named BanMMV CP9, compatible with Poty1, an oligodT reverse primer already used in diagnostics, was designed. A retrospective analysis of 110 different germplasm accessions from diverse origins was conducted, comparing BanMMCP2 and BanMMV CP9 primers. Of these 110 accessions, 16 tested positive with both BanMMCP2 and BanMMV CP9, 3 were positive with only BanMMCP2 and 2 tested positive with only BanMMV CP9. Otherwise, 89 were negative with the two primers and free of flexuous virions. Sanger sequencing was performed from purified PCR products in order to confirm the amplification of the BanMMV sequence for the five accessions with contrasting results. It is highly recommended to use the two primers successively to improve the inclusiveness of the protocol.
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Affiliation(s)
- Marwa Hanafi
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
- Correspondence:
| | - Rachid Tahzima
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
| | - Sofiene Ben Kaab
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
| | - Lucie Tamisier
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
| | - Nicolas Roux
- Consultative Group on International Agricultural Research, 34090 Montpellier, France;
| | - Sébastien Massart
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
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9
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Paniagua Voirol LR, Valsamakis G, Yu M, Johnston PR, Hilker M. How the 'kitome' influences the characterization of bacterial communities in lepidopteran samples with low bacterial biomass. J Appl Microbiol 2020; 130:1780-1793. [PMID: 33128818 DOI: 10.1111/jam.14919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/02/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022]
Abstract
AIMS We aimed to elucidate whether the DNA extraction kit and bacteria therein affect the characterization of bacterial communities associated with butterfly samples harbouring different bacterial abundancies. METHODS AND RESULTS We analysed bacteria associated with eggs of Pieris brassicae and with adults of this butterfly, which were either untreated or treated with antibiotics (ABs). Three DNA extraction kits were used. Regardless of the extraction kit used, PCR amplification of the bacterial 16S rRNA gene detected very low bacterial presence in eggs and AB-treated butterflies. In untreated butterflies, bacterial signal intensity varied according to the kit and primers used. Sequencing (MiSeq) of the bacterial communities in untreated and AB-treated butterflies revealed a low alpha diversity in untreated butterflies because of the dominance of few bacteria genera, which were detectable regardless of the kit. However, a significantly greater alpha diversity was found in AB-treated butterflies, evidencing a true bias of the results due to bacterial contaminants in the kit. CONCLUSIONS The so-called 'kitome' can impact the profiling of Lepidoptera-associated bacteria in samples with low bacterial biomass. SIGNIFICANCE AND IMPACT OF THE STUDY Our study highlights the necessity of method testing and analysis of negative controls when investigating Lepidoptera-associated bacterial communities.
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Affiliation(s)
- L R Paniagua Voirol
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - G Valsamakis
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - M Yu
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - P R Johnston
- Evolutionary Biology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - M Hilker
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
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10
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Ezzedine JA, Chardon C, Jacquet S. New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance. J Microbiol Methods 2020; 175:105996. [PMID: 32598974 DOI: 10.1016/j.mimet.2020.105996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
Appropriate use and specific primers are important in assessing the diversity and abundance of microbial groups of interest. Bdellovibrio and like organisms (BALOs), that refer to obligate Gram-negative bacterial predators of other Gram-negative bacteria, evolved in terms of taxonomy and classification over the past two decades. Hence, some former primers have become inadequate while others are yet to be designed, for both PCR (especially with the advent of NGS) and qPCR approaches. Thus, to study BALOs' abundance and diversity in a variety of aquatic ecosystems, we designed in silico specific primer sets for each BALO genera and tested them in vitro on a variety of cultures and environmental samples. Also, we performed Sanger and Nano Miseq sequencing to reveal the exact degree of specificity of the most promising primers set. Here we report our success in designing specific primers for some BALOs genera, i.e. Bdellovibrio (PCR), Bacteriovorax (qPCR), Peredibacter (PCR).
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Cécile Chardon
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France.
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11
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Xiao A, Li WC, Ye Z. Effects of Fe-oxidizing bacteria (FeOB) on iron plaque formation, As concentrations and speciation in rice (Oryza sativa L.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 190:110136. [PMID: 31901806 DOI: 10.1016/j.ecoenv.2019.110136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
Large areas of the paddy fields in South China are contaminated with arsenic (As), which causes serious problems, including high As concentrations in brown rice. Three As-resistant iron-oxidizing bacteria (FeOB) namely, Bacillus sp. T2, Pseudomonas sp. Yangling I4 and Bacillus sp. TF1-3, were isolated and applied to rice grown in different As-contaminated environments to study the effects of FeOB on the As accumulation in rice and clarify the possible mechanisms involved. The results showed that FeOB inoculation significantly decreased the inorganic As concentrations in brown rice grown in pots and paddy fields by 3.7-13.3% and 4.6-12.1%, respectively. FeOB inoculation enhanced the formation of Fe plaque, which sequestered more As on the root surface. Moreover, a significantly lower level of As(III) influx was observed in the rice cultivated with FeOB than in the control. FeOB inoculation also decreased the As concentrations in pore water and the Fe(II)/Fe(III) ratio in rhizosphere soil. The present results suggest that FeOB inoculation decreased the inorganic As concentrations in brown rice by affecting the formation of Fe plaque, As(III) uptake kinetics and rhizosphere soil properties. Based on our results, FeOB inoculation could be considered a useful method to decrease inorganic As concentrations in brown rice grown in As-contaminated paddy fields.
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Affiliation(s)
- Anwen Xiao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Wai Chin Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, SAR, People's Republic of China.
| | - Zhihong Ye
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China.
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12
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Trends in designing microbial silage quality by biotechnological methods using lactic acid bacteria inoculants: a minireview. World J Microbiol Biotechnol 2019; 35:76. [PMID: 31054017 PMCID: PMC6499736 DOI: 10.1007/s11274-019-2649-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/26/2019] [Indexed: 11/23/2022]
Abstract
Ensiling is one of the best known method to preserve fodder. The forage before ensiling intended for silages usually contains a low number of lactic acid bacteria (LAB), so it is necessary to apply starter cultures of selected strains. Traditionally, LAB starter cultures were applied to lower the pH by producing lactic acid and to inhibit the growth of undesirable epiphytic microorganisms by competing for nutrients. Nowadays, LAB inoculants have become an effective tool for creating microbial quality of silages by selecting species with extraordinary features. Epiphytic microflora characteristic of plant material used for the production of silages and the sources of undesirable microflora in the ensiling process are discussed. This review focuses on the most frequently studied issues related to the microbial silage quality and the recent trends in increasing the quality by LAB inoculants, with respect to recent directions for selecting types of modern LAB for inoculation. Among them, the main trends described were prevention of the growth of filamentous fungi and detoxification of mycotoxins by LAB inoculants, inhibition of yeast growth by LAB present in preparations and limiting the development of pathogenic bacterial microflora through controlled fermentation with the participation of LAB and the presence of their metabolites.
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Vargas-Albores F, Martínez-Córdova LR, Martínez-Porchas M, Calderón K, Lago-Lestón A. Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnol Genet Eng Rev 2018; 35:69-91. [PMID: 30221593 DOI: 10.1080/02648725.2018.1513230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.
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Affiliation(s)
- Francisco Vargas-Albores
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Luis R Martínez-Córdova
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
| | - Marcel Martínez-Porchas
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Kadiya Calderón
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
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Xie C, Zeng H, Wang C, Xu Z, Qin L. Volatile flavour components, microbiota and their correlations in different sufu, a Chinese fermented soybean food. J Appl Microbiol 2018; 125:1761-1773. [PMID: 30133098 DOI: 10.1111/jam.14078] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/11/2018] [Accepted: 08/16/2018] [Indexed: 12/25/2022]
Abstract
AIM To investigate the volatile flavour components (VFCs), microbiota and their correlations of three categories of sufu, a Chinese fermented soybean food. METHODS AND RESULTS The VFCs were analyzed by headspace solid-phase micro-extraction (HS-SPME) combined with gas chromatography and mass spectrometry. A total of 141 VFCs were tentatively identified, in which 12 esters, eight aldehydes, five alcohols and nine miscellaneous compounds were recognized as the characteristic VFCs through the relative odour activity value. The complex microbial community was revealed by Illumina MiSeq sequencing. Among the total 202 bacteria and 125 fungi species identified, 16 bacteria and 7 fungi species were revealed as dominant community members. Furthermore, the VFC-microbiota correlation was characterized by Spearman's rank correlation coefficients (ρ). Based on the positive VFC-microbiota correlation, two bacterial species and three fungal species were selected as potential flavour-producing microbiota. CONCLUSIONS A variety of VFCs and complicated microbiota were observed in the three categories of sufu. Lactococcus lactis, Sphingobacterium sp., Pichia fermentans, Kodamaea ohmeri and Saccharomyces rouxii were the potential flavour-producing microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY The preliminary results would be useful for designing starter cultures to produce sufu with desirable sensory properties, consistent flavour and shorter ripening time. Furthermore, these results will also provide a new insight to improve the flavour quality of traditional fermented soybean food.
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Affiliation(s)
- C Xie
- College of Life Science, Guizhou University, Guiyang, China
| | - H Zeng
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - C Wang
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Z Xu
- Department of Food Science, Louisiana State University, Baton Rouge, LA, USA
| | - L Qin
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Key Laboratory of Agricultural and Animal Products Storage and Processing of Guizhou Province, Guiyang, China
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Mancabelli L, Milani C, Lugli GA, Turroni F, Cocconi D, van Sinderen D, Ventura M. Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis. FEMS Microbiol Ecol 2018; 93:4604777. [PMID: 29126267 DOI: 10.1093/femsec/fix153] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/07/2017] [Indexed: 12/28/2022] Open
Abstract
Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Deborah Cocconi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Campos MJ, Quesada A. Strategies to Improve Efficiency and Specificity of Degenerate Primers in PCR. Methods Mol Biol 2018; 1620:75-85. [PMID: 28540700 DOI: 10.1007/978-1-4939-7060-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PCR with degenerate primers can be used to identify the coding sequence of an unknown protein or to detect a genetic variant within a gene family. These primers, which are complex mixtures of slightly different oligonucleotide sequences, can be optimized to increase the efficiency and/or specificity of PCR in the amplification of a sequence of interest by the introduction of mismatches with the target sequence and balancing their position toward the primers 5'- or 3'-ends. In this work, we explain in detail examples of rational design of primers in two different applications, including the use of specific determinants at the 3'-end, to: (1) improve PCR efficiency with coding sequences for members of a protein family by fully degeneration at a core box of conserved genetic information, with the reduction of degeneration at the 5'-end, and (2) optimize specificity of allelic discrimination of closely related orthologous by 5'-end degenerate primers.
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Affiliation(s)
- Maria Jorge Campos
- MARE - Marine and Environmental Sciences Centre, ESTM, Instituto Politécnico de Leiria, Apartado 4133, 2520-641, Peniche, Portugal.
| | - Alberto Quesada
- Facultad de Veterinaria, Departamento de Bioquímica, Biología Molecular y Genética, Universidad de Extremadura, Extremadura, Spain
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Soundharrajan I, Kim DH, Srisesharam S, Kuppusamy P, Park HS, Yoon YH, Kim WH, Song YG, Choi KC. Application of customised bacterial inoculants for grass haylage production and its effectiveness on nutrient composition and fermentation quality of haylage. 3 Biotech 2017; 7:321. [PMID: 28955618 DOI: 10.1007/s13205-017-0965-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/07/2017] [Indexed: 01/28/2023] Open
Abstract
The present study aimed to investigate the efficacy of customised Lactobacillus plantarum KCC-10, KCC-19 and K-46 on nutrient composition and fermentation quality of low moisture Italian ryegrass (IRG) forage. An addition of customised bacterial inoculants (CBI) did not affect the nutrient compositions and digestibility rates of haylage. The lactic acid content was higher in CBI-inoculated haylage, whereas the amount of acetic acid and butyric acid production was significantly reduced than the control. CBI-inoculated haylage exhibited higher numbers of bacterial colonies that reduced the pH of the haylage. Low pH in haylage is an important criterion for preventing undesirable microbial growth and improves fermentation quality of haylage. PCR studies indicated that the DNA of L. plantarum was predominantly amplified. It evidenced that the CBI is the main reason behind the improvement of haylage fermentation as compared to control. Overall results suggested that KCC-10, KCC-19 and K-46 are considered as potent strains for improving fermentation quality of low moisture forage and preserve its stability for a long time.
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Sun D, Duan C, Shang Y, Ma Y, Tan L, Zhai J, Gao X, Guo J, Wang G. Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7639-7647. [PMID: 26743644 DOI: 10.1007/s11356-015-6024-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
The aim of this study was to judge the legal duty of pollution liabilities by assessing a duck faeces-specific marker, which can exclude distractions of residual bacteria from earlier contamination accidents. With the gene sequencing technology and bioinformatics method, we completed the comparative analysis of Faecalibacterium sequences, which were associated with ducks and other animal species, and found the sequences unique to duck faeces. Polymerase chain reaction (PCR) and agarose gel electrophoresis techniques were used to verify the reliability of both human and duck faeces-specific primers. The duck faeces-specific primers generated an amplicon of 141 bp from 43.3 % of duck faecal samples, 0 % of control samples and 100 % of sewage wastewater samples that contained duck faeces. We present here the initial evidence of Faecalibacterium-based applicability as human faeces-specificity in China. Meanwhile, this study represents the initial report of a Faecalibacterium marker for duck faeces and suggests an independent or supplementary environmental biotechnology of microbial source tracking (MST).
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Affiliation(s)
- Da Sun
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Chuanren Duan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China.
| | - Yaning Shang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Yunxia Ma
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Lili Tan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China
| | - Jun Zhai
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, College of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
| | - Xu Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, College of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
| | - Jingsong Guo
- Key Laboratory of Reservoir Aquatic Environment of CAS, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Guixue Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), State and Local Joint Engineering Laboratory for Vascular Implants (Chongqing), Bioengineering College of Chongqing University, Chongqing University, Chongqing, China.
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Pholsen S, Khota W, Pang H, Higgs D, Cai Y. Characterization and application of lactic acid bacteria for tropical silage preparation. Anim Sci J 2016; 87:1202-1211. [DOI: 10.1111/asj.12534] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/17/2015] [Accepted: 08/04/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Suradej Pholsen
- Faculty of Agriculture; Khon Kaen University; Khon Kaen Thailand
| | - Waroon Khota
- Faculty of Agriculture; Khon Kaen University; Khon Kaen Thailand
| | - Huili Pang
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering; Zhengzhou University; Zhengzhou Henan China
| | - David Higgs
- Department of Human and Environmental Sciences; University of Hertfordshire; Hertfordshire UK
| | - Yimin Cai
- Japan International Research Center for Agricultural Sciences; Tsukuba Ibaraki Japan
- National Institute of Livestock and Grassland Science; Tsukuba Ibaraki Japan
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Ni K, Wang Y, Cai Y, Pang H. Natural Lactic Acid Bacteria Population and Silage Fermentation of Whole-crop Wheat. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1123-32. [PMID: 26104520 PMCID: PMC4478480 DOI: 10.5713/ajas.14.0955] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/27/2015] [Accepted: 03/02/2015] [Indexed: 12/03/2022]
Abstract
Winter wheat is a suitable crop to be ensiled for animal feed and China has the largest planting area of this crop in the world. During the ensiling process, lactic acid bacteria (LAB) play the most important role in the fermentation. We investigated the natural population of LAB in whole-crop wheat (WCW) and examined the quality of whole-crop wheat silage (WCWS) with and without LAB inoculants. Two Lactobacillus plantarum subsp. plantarum strains, Zhengzhou University 1 (ZZU 1) selected from corn and forage and grass 1 (FG 1) from a commercial inoculant, were used as additives. The silages inoculated with LAB strains (ZZU 1 and FG 1) were better preserved than the control, with lower pH values (3.5 and 3.6, respectively) (p<0.05) and higher contents of lactic acid (37.5 and 34.0 g/kg of fresh matter (FM), respectively) (p<0.05) than the control. Sixty LAB strains were isolated from fresh material and WCWS without any LAB inoculation. These LAB strains were divided into the following four genera and six species based on their phenotypic, biochemical and phylogenetic characteristics: Leuconostoc pseudomesenteroides, Leuconostoc citreum, Weissella cibaria, Lactococcus lactis subsp. lactis, Lactobacillus buchneri, and Lactobacillus plantarum subsp. plantarum. However, the prevalent LAB, which was predominantly heterofermentative (66.7%), consisted of Leuconostoc pseudomesenteroides, Leuconostoc citreum, Weissella cibaria, and Lactobacillus buchneri. This study revealed that most of isolated LAB strains from control WCWS were heterofermentative and could not grow well at low pH condition; the selective inoculants of Lactobacillus strains, especially ZZU 1, could improve WCWS quality significantly.
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Affiliation(s)
- Kuikui Ni
- National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
| | - Yanping Wang
- National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
| | - Yimin Cai
- National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
| | - Huili Pang
- National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
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Li D, Ni K, Pang H, Wang Y, Cai Y, Jin Q. Identification and antimicrobial activity detection of lactic Acid bacteria isolated from corn stover silage. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:620-31. [PMID: 25924957 PMCID: PMC4412991 DOI: 10.5713/ajas.14.0439] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/06/2014] [Accepted: 11/04/2014] [Indexed: 11/27/2022]
Abstract
A total of 59 lactic acid bacteria (LAB) strains were isolated from corn stover silage. According to phenotypic and chemotaxonomic characteristics, 16S ribosomal DNA (rDNA) sequences and recA gene polymerase chain reaction amplification, these LAB isolates were identified as five species: Lactobacillus (L.) plantarum subsp. plantarum, Pediococcus pentosaceus, Enterococcus mundtii, Weissella cibaria and Leuconostoc pseudomesenteroides, respectively. Those strains were also screened for antimicrobial activity using a dual-culture agar plate assay. Based on excluding the effects of organic acids and hydrogen peroxide, two L. plantarum subsp. plantarum strains ZZU 203 and 204, which strongly inhibited Salmonella enterica ATCC 43971T, Micrococcus luteus ATCC 4698T and Escherichia coli ATCC 11775T were selected for further research on sensitivity of the antimicrobial substance to heat, pH and protease. Cell-free culture supernatants of the two strains exhibited strong heat stability (60 min at 100°C), but the antimicrobial activity was eliminated after treatment at 121°C for 15 min. The antimicrobial substance remained active under acidic condition (pH 2.0 to 6.0), but became inactive under neutral and alkaline condition (pH 7.0 to 9.0). In addition, the antimicrobial activities of these two strains decreased remarkably after digestion by protease K. These results preliminarily suggest that the desirable antimicrobial activity of strains ZZU 203 and 204 is the result of the production of a bacteriocin-like substance, and these two strains with antimicrobial activity could be used as silage additives to inhibit proliferation of unwanted microorganism during ensiling and preserve nutrients of silage. The nature of the antimicrobial substances is being investigated in our laboratory.
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Affiliation(s)
- Dongxia Li
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering, Zhengzhou University, Zhengzhou 450052, China
| | - Kuikui Ni
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering, Zhengzhou University, Zhengzhou 450052, China
| | - Huili Pang
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering, Zhengzhou University, Zhengzhou 450052, China
| | - Yanping Wang
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering, Zhengzhou University, Zhengzhou 450052, China
| | - Yimin Cai
- Animal Physiology and Nutrition Division, National Institute of Livestock and Grassland Science, Tsukuba 305-0901, Japan
| | - Qingsheng Jin
- Institute of Crops and Utilization of Nuclear Technology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Sebastião FA, Furlan LR, Hashimoto DT, Pilarski F. Identification of Bacterial Fish Pathogens in Brazil by Direct Colony PCR and 16S rRNA Gene Sequencing. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/aim.2015.56042] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Wu JJ, Du RP, Gao M, Sui YQ, Xiu L, Wang X. Naturally occurring lactic Acid bacteria isolated from tomato pomace silage. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:648-57. [PMID: 25049999 PMCID: PMC4093187 DOI: 10.5713/ajas.2013.13670] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/24/2013] [Accepted: 01/12/2014] [Indexed: 12/03/2022]
Abstract
Silage making has become a significant method of forage conservation worldwide. To determine how tomato pomace (TP) may be used effectively as animal feed, it was ensilaged for 90 days and microbiology counts, fermentation characteristics and chemical composition of tomato pomace silage (TPS) were evaluated at the 30th, 60th, and 90th days, respectively. In addition, 103 lactic acid bacteria were isolated from TPS. Based on the phenotypic and chemotaxonomic characteristics, 16S rDNA sequence and carbohydrate fermentation tests, the isolates were identified as 17 species namely: Lactobacillus coryniformis subsp. torquens (0.97%), Lactobacillus pontis (0.97%), Lactobacillus hilgardii (0.97%), Lactobacillus pantheris (0.97%), Lactobacillus amylovorus (1.9%), Lactobacillus panis (1.9%), Lactobacillus vaginalis (1.9%), Lactobacillus rapi (1.9%), Lactobacillus buchneri (2.9%), Lactobacillus parafarraginis (2.9%), Lactobacillus helveticus (3.9%), Lactobacillus camelliae (3.9%), Lactobacillus fermentum (5.8%), Lactobacillus manihotivorans (6.8%), Lactobacillus plantarum (10.7%), Lactobacillus harbinensis (16.5%) and Lactobacillus paracasei subsp. paracasei (35.0%). This study has shown that TP can be well preserved for 90 days by ensilaging and that TPS is not only rich in essential nutrients, but that physiological and biochemical properties of the isolates could provide a platform for future design of lactic acid bacteria (LAB) inoculants aimed at improving the fermentation quality of silage.
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Affiliation(s)
- Jing-Jing Wu
- Animal Nutrition Institute of Agriculture and Animal Husbandry Academy of Inner Mongolia, Huhhot 010031, China
| | - Rui-Ping Du
- Animal Nutrition Institute of Agriculture and Animal Husbandry Academy of Inner Mongolia, Huhhot 010031, China
| | - Min Gao
- Animal Nutrition Institute of Agriculture and Animal Husbandry Academy of Inner Mongolia, Huhhot 010031, China
| | - Yao-Qiang Sui
- Animal Nutrition Institute of Agriculture and Animal Husbandry Academy of Inner Mongolia, Huhhot 010031, China
| | - Lei Xiu
- Animal Nutrition Institute of Agriculture and Animal Husbandry Academy of Inner Mongolia, Huhhot 010031, China
| | - Xiao Wang
- Animal Nutrition Institute of Agriculture and Animal Husbandry Academy of Inner Mongolia, Huhhot 010031, China
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Identification and phylogenetic characterization of novel Lactobacillus plantarum species and their metabolite profiles in grass silage. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0830-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Wu JJ, Du RP, Gao M, Sui YQ, Wang X. Identification and characterization of lactic acid bacteria isolated from tomato pomace. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-013-0798-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Hernandez-Sanabria E, Goonewardene LA, Wang Z, Zhou M, Moore SS, Guan LL. Influence of sire breed on the interplay among rumen microbial populations inhabiting the rumen liquid of the progeny in beef cattle. PLoS One 2013; 8:e58461. [PMID: 23520513 PMCID: PMC3592819 DOI: 10.1371/journal.pone.0058461] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 02/04/2013] [Indexed: 01/08/2023] Open
Abstract
This study aimed to evaluate whether the host genetic background impact the ruminal microbial communities of the progeny of sires from three different breeds under different diets. Eighty five bacterial and twenty eight methanogen phylotypes from 49 individuals of diverging sire breed (Angus, ANG; Charolais, CHA; and Hybrid, HYB), fed high energy density (HE) and low energy density (LE) diets were determined and correlated with breed, rumen fermentation and phenotypic variables, using multivariate statistical approaches. When bacterial phylotypes were compared between diets, ANG offspring showed the lowest number of diet-associated phylotypes, whereas CHA and HYB progenies had seventeen and twenty-three diet-associated phylotypes, respectively. For the methanogen phylotypes, there were no sire breed-associated phylotypes; however, seven phylotypes were significantly different among breeds on either diet (P<0.05). Sire breed did not influence the metabolic variables measured when high energy diet was fed. A correlation matrix of all pairwise comparisons among frequencies of bacterial and methanogen phylotypes uncovered their relationships with sire breed. A cluster containing methanogen phylotypes M16 (Methanobrevibacter gottschalkii) and M20 (Methanobrevibacter smithii), and bacterial phylotype B62 (Robinsoniella sp.) in Angus offspring fed low energy diet reflected the metabolic interactions among microbial consortia. The clustering of the phylotype frequencies from the three breeds indicated that phylotypes detected in CHA and HYB progenies are more similar among them, compared to ANG animals. Our results revealed that the frequency of particular microbial phylotypes in the progeny of cattle may be influenced by the sire breed when different diets are fed and ultimately further impact host metabolic functions, such as feed efficiency.
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Affiliation(s)
- Emma Hernandez-Sanabria
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Laksiri A. Goonewardene
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen S. Moore
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- The University of Queensland Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, Queensland, Australia
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Abstract
Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n=5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR (P less than 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.
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Sanuth HA, Yadav A, Fagade OE, Shouche Y. ε-Caprolactam Utilization by Proteus sp. and Bordetella sp. Isolated From Solid Waste Dumpsites in Lagos State, Nigeria, First Report. Indian J Microbiol 2013; 53:221-6. [PMID: 24426112 DOI: 10.1007/s12088-013-0356-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/04/2013] [Indexed: 10/27/2022] Open
Abstract
The ε-caprolactam is the monomer of the synthetic non-degradable nylon-6 and often found as nonreactive component of nylon-6 manufacturing waste effluent. Environmental consequences of its toxicity to natural habitats and humans pose a global public concern. Soil samples were collected from three designated solid waste dumpsites, namely, Abule-Egba, Olusosun and Isheri-Igando in Lagos State, Nigeria. Sixteen bacteria isolated from these samples were found to utilize the ε-caprolactam as a sole source of carbon and nitrogen at concentration of ≤20 g l(-1). The isolates were characterized using their 16S rRNA gene sequence and showed similarity with Pseudomonas sp., Proteus sp., Providencia sp., Corynebacterium sp., Lysinibacillus sp., Leucobacter sp., Alcaligenes sp. and Bordetella sp. Their optimal growth conditions were found to be at temperature range of 30 to 35 °C and pH range of 7.0-7.5. High Performance liquid chromatography analysis of the ε-caprolactam from supernatant of growth medium revealed that these isolates have potential to remove 31.6-95.7 % of ε-caprolactam. To the best of our knowledge, this study is first to report the ability of Proteus sp. and Bordetella sp. for ε-caprolactam utilization.
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Affiliation(s)
- Hassan Adeyemi Sanuth
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Oyo State Nigeria
| | - Amit Yadav
- Microbial Culture Collection, National Centre for Cell Science (NCCS) Complex, Ganeshkhind, Pune, 411007 Maharashtra India
| | - Obasola Ezekiel Fagade
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Oyo State Nigeria
| | - Yogesh Shouche
- Microbial Culture Collection, National Centre for Cell Science (NCCS) Complex, Ganeshkhind, Pune, 411007 Maharashtra India
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29
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Marathe N, Shetty S, Lanjekar V, Ranade D, Shouche Y. Changes in human gut flora with age: an Indian familial study. BMC Microbiol 2012; 12:222. [PMID: 23013146 PMCID: PMC3511239 DOI: 10.1186/1471-2180-12-222] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 09/13/2012] [Indexed: 12/31/2022] Open
Abstract
Background The gut micro flora plays vital role in health status of the host. The majority of microbes residing in the gut have a profound influence on human physiology and nutrition. Different human ethnic groups vary in genetic makeup as well as the environmental conditions they live in. The gut flora changes with genetic makeup and environmental factors and hence it is necessary to understand the composition of gut flora of different ethnic groups. Indian population is different in physiology from western population (YY paradox) and thus the gut flora in Indian population is likely to differ from the extensively studied gut flora in western population. In this study we have investigated the gut flora of two Indian families, each with three individuals belonging to successive generations and living under the same roof. Results Denaturation gradient gel electrophoresis analysis showed age-dependant variation in gut microflora amongst the individuals within a family. Different bacterial genera were dominant in the individual of varying age in clone library analysis. Obligate anaerobes isolated from individuals within a family showed age related differences in isolation pattern, with 27% (6 out of 22) of the isolates being potential novel species based on 16S rRNA gene sequence. In qPCR a consistent decrease in Firmicutes number and increase in Bacteroidetes number with increasing age was observed in our subjects, this pattern of change in Firmicutes / Bacteroidetes ratio with age is different than previously reported in European population. Conclusion There is change in gut flora with age amongst the individuals within a family. The isolation of high percent of novel bacterial species and the pattern of change in Firmicutes /Bacteroidetes ratio with age suggests that the composition of gut flora in Indian individuals may be different than the western population. Thus, further extensive study is needed to define the gut flora in Indian population.
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Affiliation(s)
- Nachiket Marathe
- 1Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune- 411 007, Maharashtra, India
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Valverde A, Tuffin M, Cowan DA. Biogeography of bacterial communities in hot springs: a focus on the actinobacteria. Extremophiles 2012; 16:669-79. [PMID: 22711422 DOI: 10.1007/s00792-012-0465-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 05/25/2012] [Indexed: 11/26/2022]
Abstract
Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5 °C and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.
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Affiliation(s)
- Angel Valverde
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, Cape Town 7535, South Africa
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31
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Capturing greater 16S rRNA gene sequence diversity within the domain Bacteria. Appl Environ Microbiol 2012; 78:5938-41. [PMID: 22685133 DOI: 10.1128/aem.01299-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large proportion of "universal" 16S PCR primers lack sequence homology to many of the "candidate" divisions, severely limiting bacterial diversity assessments. We designed a primer set that offers a 50% increase in silico in coverage of the domain Bacteria over the commonly used primer combination 27F/519R. Comparisons using pyrosequencing on soil environments showed a significant increase in recovery of taxonomic diversity with around a 3-fold increase in recovery of sequences from candidate divisions.
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32
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Mukhopadhyay J, Braig HR, Rowton ED, Ghosh K. Naturally occurring culturable aerobic gut flora of adult Phlebotomus papatasi, vector of Leishmania major in the Old World. PLoS One 2012; 7:e35748. [PMID: 22629302 PMCID: PMC3358311 DOI: 10.1371/journal.pone.0035748] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/23/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cutaneous leishmaniasis is a neglected, vector-borne parasitic disease and is responsible for persistent, often disfiguring lesions and other associated complications. Leishmania, causing zoonotic cutaneous leishmaniasis (ZCL) in the Old World are mainly transmitted by the predominant sand fly vector, Phlebotomus papatasi. To date, there is no efficient control measure or vaccine available for this widespread insect-borne infectious disease. METHODOLOGY/PRINCIPAL FINDINGS A survey was carried out to study the abundance of different natural gut flora in P. papatasi, with the long-term goal of generating a paratransgenic sand fly that can potentially block the development of Leishmania in the sand fly gut, thereby preventing transmission of leishmania in endemic disease foci. Sand flies, in particular, P. papatasi were captured from different habitats of various parts of the world. Gut microbes were cultured and identified using 16S ribosomal DNA analysis and a phylogenetic tree was constructed. We found variation in the species and abundance of gut flora in flies collected from different habitats. However, a few Gram-positive, nonpathogenic bacteria including Bacillus flexus and B. pumilus were common in most of the sites examined. CONCLUSION/SIGNIFICANCE Our results indicate that there is a wide range of variation of aerobic gut flora inhabiting sand fly guts, which possibly reflect the ecological condition of the habitat where the fly breeds. Also, some species of bacteria (B. pumilus, and B. flexus) were found from most of the habitats. Important from an applied perspective of dissemination, our results support a link between oviposition induction and adult gut flora.
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Affiliation(s)
- Jaba Mukhopadhyay
- Division of Entomology, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Henk R. Braig
- School of Biological Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Edgar D. Rowton
- Division of Entomology, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Kashinath Ghosh
- Division of Entomology, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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33
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Cai Y, Pang H, Kitahara M, Ohkuma M. Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus. Int J Syst Evol Microbiol 2012; 62:1140-1144. [DOI: 10.1099/ijs.0.031781-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of lactic acid bacteria, designated SU 18T and SU 83, were isolated from silage prepared with Sudan grass [Sorghum sudanense (Piper) Stapf.]. The isolates were Gram-stain-positive, catalase-negative, facultatively anaerobic rods that did not produce gas from glucose. The isolates exhibited ≥93.5 % DNA–DNA relatedness to each other and shared the same phenotypic characteristics, which indicated that they belonged to a single species. The DNA G+C content was 58.5–59.2 mol%. On the basis of 16S rRNA gene sequence analysis, the isolates were placed in the genus
Lactobacillus
. Their closest phylogenetic neighbours were
Lactobacillus manihotivorans
JCM 12514T and
Lactobacillus camelliae
JCM 13995T (95.9 and 96.8 % 16S rRNA gene sequence similarity, respectively, with strain SU 18T). Ribotyping revealed that strain SU 18T was well separated from
L. manihotivorans
JCM 12514T and
L. camelliae
JCM 13995T. Strain SU 18T exhibited ≤23.7 % DNA–DNA relatedness with its closest phylogenetic neighbours. The isolates represent a novel species in the genus
Lactobacillus
, for which the name Lactobacillus nasuensis sp. nov. is proposed. The type strain is SU 18T ( = JCM 17158T = CGMCC 1.10801T). The description of the genus
Lactobacillus
is also amended.
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Affiliation(s)
- Yimin Cai
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Huili Pang
- Zhengzhou University, Zhengzhou, Henan 450052, PR China
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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34
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Ben-Dov E, Shapiro OH, Kushmaro A. 'Next-base' effect on PCR amplification. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:183-188. [PMID: 23757271 DOI: 10.1111/j.1758-2229.2011.00318.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The base adjacent to the 3' end of universal PCR primers targeting the 16S rRNA gene is often variable and apparently biases the microbial community composition as represented by PCR-based surveys. To test this hypothesis, four templates of 44 bases each and two complementary primers (21 bases) were designed to differ only in the bases adjacent to the primers, and their amplification efficiencies were evaluated using quantitative PCR. For extension temperatures of 72°C, 73°C and 74°C, improvement in initial amplification efficiency was observed for templates with guanine or cytosine at the position contiguous to the primers. However, no clear preference was observed when extension temperature was lowered to 70°C. Shortening the primers by one base, so that the variable position was located two base pairs downstream from the primer, attenuated but did not eliminate this bias. A conformational change of the quaternary polymerase - primer - template - dNTP complex upon commencing of polymerization is thought to be a rate-limiting step. A possible explanation for the observed bias is the stabilization of this complex by the adjacent guanine or cytosine. Reducing PCR extension temperature to 70°C minimizes amplification biases caused by variable template-contiguous bases to the 3' end of universal PCR primers. Next-base nucleotide composition should be taken in consideration in designing primers targeting 16S rRNA or other functional genes used in microbial ecology studies.
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Affiliation(s)
- Eitan Ben-Dov
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, PO Box 653, Be'er Sheva 84105, Israel Achva Academic College MP Shikmim, 79800, Israel National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, PO Box 653, Be'er-Sheva 84105, Israel School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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35
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Pang H, Tan Z, Qin G, Wang Y, Li Z, Jin Q, Cai Y. Phenotypic and phylogenetic analysis of lactic acid bacteria isolated from forage crops and grasses in the Tibetan Plateau. J Microbiol 2012; 50:63-71. [PMID: 22367939 DOI: 10.1007/s12275-012-1284-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 10/31/2011] [Indexed: 11/26/2022]
Abstract
A total of 140 lactic acid bacteria (LAB) strains were isolated from corn, alfalfa, clover, sainfoin, and Indian goosegrass in the Tibetan Plateau. According to phenotypic and chemotaxonomic characteristics, 16S rDNA sequence, and recA gene PCR amplification, these LAB isolates were identified as belonging to five genera and nine species. Corn contained more LAB species than other forage crops. Leuconostoc pseudomesenteroides, Lactococcus lactis subsp. lactis, Lactobacillus brevis, and Weissella paramesenteroides were dominant members of the LAB population on alfalfa, clover, sainfoin, and Indian goosegrass, respectively. The comprehensive 16S rDNA and recA-based approach effectively described the LAB community structure of the relatively abundant LAB species distributed on different forage crops. This is the first report describing the diversity and natural populations of LAB associated with Tibetan forage crops, and most isolates grow well at or below 10°C. The results will be valuable for the future design of appropriate inoculants for silage fermentation in this very cold area.
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Affiliation(s)
- Huili Pang
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering, Zhengzhou University, 450052, Zhengzhou, Henan, P. R. China
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36
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Impact of feed efficiency and diet on adaptive variations in the bacterial community in the rumen fluid of cattle. Appl Environ Microbiol 2011; 78:1203-14. [PMID: 22156428 DOI: 10.1128/aem.05114-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Limited knowledge of the structure and activities of the ruminal bacterial community prevents the understanding of the effect of population dynamics on functional bacterial groups and on host productivity. This study aimed to identify particular bacteria associated with host feed efficiency in steers with differing diets and residual feed intake (RFI) using culture-independent methods: PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis. PCR-DGGE profiles were generated from the ruminal fluid of 55 steers fed a low-energy-density diet and then switched to a high-energy-density diet. Bacterial profile comparisons by multivariate statistical analysis showed a trend only for RFI-related clusters on the high-energy diet. When steers (n = 19) belonging to the same RFI group under both diets were used to identify specific bacterial phylotypes related to feed efficiency traits, correlations were detected between dry matter intake, average daily gain, and copy numbers of the 16S rRNA gene of Succinivibrio sp. in low-RFI (efficient) steers, whereas correlations between Robinsoniella sp. and RFI (P < 0.05) were observed for high-RFI (inefficient) animals. Eubacterium sp. differed significantly (P < 0.05) between RFI groups that were only on the high-energy diet. Our work provides a comprehensive framework to understand how particular bacterial phylotypes contribute to differences in feed efficiency and ultimately influence host productivity, which may either depend on or be independent from diet factors.
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Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 2011; 22:299-306. [PMID: 22009989 DOI: 10.1101/gr.126516.111] [Citation(s) in RCA: 1344] [Impact Index Per Article: 103.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An estimated 15% or more of the cancer burden worldwide is attributable to known infectious agents. We screened colorectal carcinoma and matched normal tissue specimens using RNA-seq followed by host sequence subtraction and found marked over-representation of Fusobacterium nucleatum sequences in tumors relative to control specimens. F. nucleatum is an invasive anaerobe that has been linked previously to periodontitis and appendicitis, but not to cancer. Fusobacteria are rare constituents of the fecal microbiota, but have been cultured previously from biopsies of inflamed gut mucosa. We obtained a Fusobacterium isolate from a frozen tumor specimen; this showed highest sequence similarity to a known gut mucosa isolate and was confirmed to be invasive. We verified overabundance of Fusobacterium sequences in tumor versus matched normal control tissue by quantitative PCR analysis from a total of 99 subjects (p = 2.5 × 10(-6)), and we observed a positive association with lymph node metastasis.
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Affiliation(s)
- Mauro Castellarin
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
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38
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Changes in bacterial diversity associated with epithelial tissue in the beef cow rumen during the transition to a high-grain diet. Appl Environ Microbiol 2011; 77:5770-81. [PMID: 21705529 DOI: 10.1128/aem.00375-11] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our understanding of the ruminal epithelial tissue-associated bacterial (defined as epimural bacteria in this study) community is limited. In this study, we aimed to determine whether diet influences the diversity of the epimural bacterial community in the bovine rumen. Twenty-four beef heifers were randomly assigned to either a rapid grain adaptation (RGA) treatment (n = 18) in which the heifers were allowed to adapt from a diet containing 97% hay to a diet containing 8% hay over 29 days or to the control group (n = 6), which was fed 97% hay. Rumen papillae were collected when the heifers were fed 97%, 25%, and 8% hay diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis were used to characterize rumen epimural bacterial diversity and to estimate the total epimural bacterial population (copy numbers of the 16S rRNA gene). The epimural bacterial diversity from RGA heifers changed (P = 0.01) in response to the rapid dietary transition, whereas it was not affected in control heifers. A total of 88 PCR-DGGE bands were detected, and 44 were identified from phyla including Firmicutes, Bacteroidetes, and Proteobacteria. The bacteria Treponema sp., Ruminobacter sp., and Lachnospiraceae sp. were detected only when heifers were fed 25% and 8% hay diets, suggesting the presence of these bacteria is the result of adaptation to the high-grain diets. In addition, the total estimated population of rumen epimural bacteria was positively correlated with molar proportions of acetate, isobutyrate, and isovalerate, suggesting that they may play a role in volatile fatty acid metabolism in the rumen.
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Pang H, Zhang M, Qin G, Tan Z, Li Z, Wang Y, Cai Y. Identification of lactic acid bacteria isolated from corn stovers. Anim Sci J 2011; 82:642-53. [PMID: 21951900 DOI: 10.1111/j.1740-0929.2011.00894.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One hundred and twenty-six strains were isolated from corn stover in Henan Province, China, of which 105 isolates were considered to be lactic acid bacteria (LAB) according to Gram-positive, catalase-negative and mainly metabolic lactic acid product. Analysis of the 16S ribosomal DNA sequence of 21 representative strains was used to confirm the presence of the predominant groups and to determine the phylogenetic affiliation of isolates. The sequences from the various LAB isolates showed high degrees of similarity to those of the GenBank type strains between 99.4% and 100%. The prevalent LAB, predominantly Lactobacillus (85.6%), consisted of L. plantarum (33.3%), L. pentosus (28.6%) and L. brevis (23.7%). Other LAB species as Leuconostoc lactis (4.8%), Weissella cibaria (4.8%) and Enterococcus mundtii (4.8%) also presented in corn stover. The present study is the first to fully document corn stover-associated LAB involved in the silage fermentation. The identification results revealed LAB composition inhabiting corn stover and enabling the future design of appropriate inoculants aimed at improving the fermentation quality of silage.
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Affiliation(s)
- Huili Pang
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering, Zhengzhou University, Henan, China
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40
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41
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Thomas MC, Thomas DK, Selinger LB, Inglis GD. spyder, a new method for in silico design and assessment of 16S rRNA gene primers for molecular microbial ecology. FEMS Microbiol Lett 2011; 320:152-9. [PMID: 21554380 DOI: 10.1111/j.1574-6968.2011.02302.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Molecular microbial ecology studies are heavily reliant on 'Universal' 16S rRNA gene primers for elucidating microbial community structure and composition, and yet primer design and optimization is often overlooked. Primers that exhibit minor biases due to primer-template mismatches can substantially alter the pool of amplicons from a community DNA sample, resulting in inaccurate conclusions. As a result, it is important that primers are critically evaluated against the most comprehensive data sets available before commencing molecular microbial community studies. We present a user-friendly, multi-platform (e.g. Windows, Linux, Mac) method named spyder for the in silico design and assessment of 16S rRNA gene primers. The method utilizes the Ribosomal Database Project's Probe Match feature coupled with a compact program (available at http://people.uleth.ca/~selibl/Spyder/Spyder.html) that aligns and identifies mismatches between primers and templates. To demonstrate the value of spyder, we assessed commonly used 'Universal' and phyla-specific primers and identified primer modifications that improved the coverage of target organisms by 5-42% as well as removed excessive degeneracies.
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Pang H, Qin G, Tan Z, Li Z, Wang Y, Cai Y. Natural populations of lactic acid bacteria associated with silage fermentation as determined by phenotype, 16S ribosomal RNA and recA gene analysis. Syst Appl Microbiol 2011; 34:235-41. [DOI: 10.1016/j.syapm.2010.10.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Revised: 10/26/2010] [Accepted: 10/28/2010] [Indexed: 11/30/2022]
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Barghouthi SA. A universal method for the identification of bacteria based on general PCR primers. Indian J Microbiol 2011; 51:430-44. [PMID: 23024404 DOI: 10.1007/s12088-011-0122-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 06/22/2009] [Indexed: 11/29/2022] Open
Abstract
The Universal Method (UM) described here will allow the detection of any bacterial rDNA leading to the identification of that bacterium. The method should allow prompt and accurate identification of bacteria. The principle of the method is simple; when a pure PCR product of the 16S gene is obtained, sequenced, and aligned against bacterial DNA data base, then the bacterium can be identified. Confirmation of identity may follow. In this work, several general 16S primers were designed, mixed and applied successfully against 101 different bacterial isolates. One mixture, the Golden mixture7 (G7) detected all tested isolates (67/67). Other golden mixtures; G11, G10, G12, and G5 were useful as well. The overall sensitivity of the UM was 100% since all 101 isolates were detected yielding intended PCR amplicons. A selected PCR band from each of 40 isolates was sequenced and the bacterium identified to species or genus level using BLAST. The results of the UM were consistent with bacterial identities as validated with other identification methods; cultural, API 20E, API 20NE, or genera and species specific PCR primers. Bacteria identified in the study, covered 34 species distributed among 24 genera. The UM should allow the identification of species, genus, novel species or genera, variations within species, and detection of bacterial DNA in otherwise sterile samples such as blood, cerebrospinal fluid, manufactured products, medical supplies, cosmetics, and other samples. Applicability of the method to identifying members of bacterial communities is discussed. The approach itself can be applied to other taxa such as protists and nematodes.
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Affiliation(s)
- Sameer A Barghouthi
- Medical Laboratory Sciences, Faculty of Health Professions, Al-Quds University, West Bank, Palestinian Territory, Jerusalem, Palestine
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Ben-Dov E, Siboni N, Shapiro OH, Arotsker L, Kushmaro A. Substitution by inosine at the 3'-ultimate and penultimate positions of 16S rRNA gene universal primers. MICROBIAL ECOLOGY 2011; 61:1-6. [PMID: 20614115 DOI: 10.1007/s00248-010-9718-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 06/23/2010] [Indexed: 05/29/2023]
Abstract
Universal 16S rRNA gene primers (8F and 518R) bearing inosine substitutions at either the 3'-ultimate or the 3'-ultimate and penultimate base positions were exploited for the first time to study the bacterial community associated with coral polymicrobial Black Band Disease (BBD). Inosine-modified universal primer pairs display some shifting in the composition of 16S rRNA gene libraries, as well as expanding the observed diversity of a BBD bacterial community at the family/class level. Possible explanations for the observed shifts are discussed. These results thus point to the need for adopting multiple approaches in designing 16S rRNA universal primers for PCR amplification and subsequent construction of 16S rRNA gene libraries or pyrosequencing in the exploration of complex microbial communities.
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Affiliation(s)
- Eitan Ben-Dov
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, PO Box 653, Be'er Sheva, 84105, Israel
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Brands B, Vianna ME, Seyfarth I, Conrads G, Horz HP. Complementary retrieval of 16S rRNA gene sequences using broad-range primers with inosine at the 3'-terminus: implications for the study of microbial diversity. FEMS Microbiol Ecol 2010; 71:157-67. [PMID: 19807788 DOI: 10.1111/j.1574-6941.2009.00786.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We evaluated the impact of the base analogue inosine substituted at the 3'-terminus of broad-range 16S rRNA gene primers on the recovery of microbial diversity using terminal restriction fragment length polymorphism and clonal analysis. Oral plaque biofilms from 10 individuals were tested with modified and unmodified primer pairs. Besides a core overlap of shared terminal restriction fragments (T-RFs), each primer system provided unique information on the occurrence of T-RFs, with a higher number generally displayed with inosine primers. All clones sequenced were at least 99% identical to publicly available full-length sequences. Analysis of the corresponding primer-binding sites showed that most sequence types were 100% complementary to the unmodified primers so that the characteristic of inosine to bind with all four nucleotides was not crucial for the observed increase in microbial richness. Instead, differences in community compositions were correlated with the identity of the nearest-neighbor 3' of the primer-targeting region. By influencing the thermal stability of primer hybridization, this position may play a previously unrecognized role in biased amplification of 16S rRNA gene sequences. In conclusion, the combined use of inosine and unmodified primers enables the complementary retrieval of 16S rRNA gene types, thereby expanding the observed diversity of complex microbial communities.
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Affiliation(s)
- Berit Brands
- Department of Operative and Preventive Dentistry and Periodontology, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Comparison of culture methods for isolation of nontuberculous mycobacteria from surface waters. Appl Environ Microbiol 2010; 76:3514-20. [PMID: 20363776 DOI: 10.1128/aem.02659-09] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The environment is the likely source of most nontuberculous mycobacteria (NTM) involved in human infections, especially pulmonary, skin, and soft tissue infections. In order to measure the prevalence of NTM in different aquatic ecosystems, we tried to standardize the culture methods used for surface water testing since many procedures have been described previously. Cultivation of mycobacteria requires long-term incubation in rich media and inactivation of rapidly growing microorganisms whose growth impedes observation of mycobacterial colonies. Consequently, the two criteria used for evaluation of the methods examined were (i) the rate of inhibition of nontarget microorganisms and (ii) the efficiency of recovery of mycobacteria. We compared the competitive growth of Mycobacterium chelonae and M. avium with nontarget microorganisms on rich Middlebrook 7H11-mycobactin medium after treatment by several chemical decontamination methods that included acids, bases, detergent, or cetylpyridinium chloride (CPC) with and without an antibiotic cocktail, either PANTA (40 U/ml polymyxin, 4 microg/ml amphotericin B, 16 microg/ml nalidixic acid, 4 microg/ml trimethoprim, and 4 microg/ml azlocillin) or PANTAV (PANTA plus 10 microg/ml vancomycin). Our results showed that treatment for 30 min with CPC (final concentration, 0.05%) of water concentrated by centrifugation, followed by culture on a rich medium supplemented with PANTA, significantly decreased the growth of nontarget microorganisms (the concentrations were 6.2 +/- 0.4 log(10) CFU/liter on Middlebrook 7H11j medium and 4.2 +/- 0.2 log(10) CFU/liter on Middlebrook 7H11j medium containing PANTA [P < 0.001]), while the effect of this procedure on NTM was not as great (the concentrations of M. chelonae on the two media were 7.0 +/- 0.0 log(10) CFU/liter and 6.9 +/- 0.0 log(10) CFU/liter, respectively, and the concentrations of M. avium were 9.1 +/- 0.0 log(10) CFU/liter and 8.9 +/- 0.0 log(10) CFU/liter, respectively). We propose that this standardized culture procedure could be used for detection of NTM in aquatic samples.
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Zheng G, Yampara-Iquise H, Jones JE, Andrew Carson C. Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces. J Appl Microbiol 2010; 106:634-41. [PMID: 19200327 DOI: 10.1111/j.1365-2672.2008.04037.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS The focus of this study was to identify a bacterial 16S rRNA gene sequence, unique to microbiota in the human gut, for use in development of a dependable PCR assay to detect human faecal pollution in water. METHODS AND RESULTS Suppression subtractive hybridization (SSH) and bioinformatics were used to identify a genetic marker, within the 16S rRNA gene of Faecalibacterium, for the detection of human faeces. DNA sequencing analysis demonstrated that a majority (16) of 74 clones of the SSH library contained insertion sequences identified as Faecalibacterium 16S rRNA genes. Human faeces-specific sequences were derived and six PCR primer sets designed and tested against faecal DNA samples from human and nonhuman sources. One PCR primer set, HFB-F3 and HFB-R5, was exclusively associated with human faeces. These primers generated a human faeces-specific amplicon of 399 bp from 60.2% of human faecal samples and 100% of sewage samples. CONCLUSIONS The subject Faecalibacterium marker is specific for sewage. SIGNIFICANCE AND IMPACT OF THE STUDY This study represents the initial report of a Faecalibacterium marker for human faeces, which may prove useful for microbial source tracking.
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Affiliation(s)
- G Zheng
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
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Angel R, Soares MIM, Ungar ED, Gillor O. Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME JOURNAL 2009; 4:553-63. [PMID: 20033070 DOI: 10.1038/ismej.2009.136] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For centuries, biodiversity has spellbound biologists focusing mainly on macroorganism's diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (<100 mm annual rain) to the Mediterranean forests in the north (>900 mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P=0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P=0.0001, for both domains), as well as patch type (P=0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.
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Affiliation(s)
- Roey Angel
- Zuckerberg Institute for Water Research, J. Blaustein Institutes for Desert Research, Ben-Gurion University, Sede Boqer Campus, Israel
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Shapiro OH, Kushmaro A, Brenner A. Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater. ISME JOURNAL 2009; 4:327-36. [PMID: 19924159 DOI: 10.1038/ismej.2009.118] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Changes in the microbial community composition of a full-scale membrane bioreactor treating industrial wastewater were studied over a period of 462 days using a series of 16S rRNA gene clone libraries. Frequent changes in the relative abundance of specific taxonomic groups were observed, which could not be explained by changes in the reactor's conditions or wastewater composition. Phage activity was proposed to drive some of the observed changes. Bacterial hosts were isolated from a biomass sample obtained towards the end of the study period, and specific phage counts were carried out for some of the isolated hosts using stored frozen biomass samples as the phage inocula. Plaque-forming unit concentrations were shown to change frequently over the study period, in correlation with changes in the relative abundance of taxonomic groups closely related by 16S rRNA gene sequence to the isolated strains. Quantitative PCR was used to verify changes in the abundance of a taxonomic group closely related to one of the isolated hosts, showing good agreement with the changes in relative abundance in the clone libraries of that group. The emerging pattern was consistent with the 'killing the winner' hypothesis, although alternative interaction mechanisms could not be ruled out. This is the first time that phage-host interactions in a complex microbial community are demonstrated over an extended period, and possibly the first in situ demonstration of 'killing the winner' stochastic behavior.
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Affiliation(s)
- Orr H Shapiro
- Department of Biotechnology Engineering, Faculty of Engineering Science, Ben-Gurion University of Negev, Beer-Sheva, Israel
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Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR. J Microbiol 2009; 47:393-401. [PMID: 19763412 DOI: 10.1007/s12275-009-0082-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 04/18/2009] [Indexed: 10/20/2022]
Abstract
Diversity of bacterial endophytes associated with grapevine leaf tissues was analyzed by cultivation and cultivation-independent methods. In order to identify bacterial endophytes directly from metagenome, a protocol for bacteria enrichment and DNA extraction was optimized. Sequence analysis of 16S rRNA gene libraries underscored five diverse Operational Taxonomic Units (OTUs), showing best sequence matches with gamma-Proteobacteria, family Enterobacteriaceae, with a dominance of the genus Pantoea. Bacteria isolation through cultivation revealed the presence of six OTUs, showing best sequence matches with Actinobacteria, genus Curtobacterium, and with Firmicutes genera Bacillus and Enterococcus. Length Heterogeneity-PCR (LH-PCR) electrophoretic peaks from single bacterial clones were used to setup a database representing the bacterial endophytes identified in association with grapevine tissues. Analysis of healthy and phytoplasma-infected grapevine plants showed that LH-PCR could be a useful complementary tool for examining the diversity of bacterial endophytes especially for diversity survey on a large number of samples.
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