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Gonzalez E, Pitre FE, Brereton NJB. ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples. Environ Microbiol 2019; 21:2440-2468. [PMID: 30990927 PMCID: PMC6851558 DOI: 10.1111/1462-2920.14632] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/07/2019] [Accepted: 04/15/2019] [Indexed: 01/04/2023]
Abstract
Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.
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Affiliation(s)
- Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, H3A 0G1, Canada.,Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.,Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
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Bae KS, Kim MS, Lee JH, Kang JW, Kim DI, Lee JH, Seong CN. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria. J Microbiol 2016; 54:789-795. [PMID: 27888457 DOI: 10.1007/s12275-016-6446-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/02/2016] [Indexed: 11/26/2022]
Abstract
To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.
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Affiliation(s)
- Kyung Sook Bae
- Biological Resource Center, KRIBB, Jeongeup, 56212, Republic of Korea
| | - Mi Sun Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea.
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Affiliation(s)
- Michio Tsukamura
- National Sanatorium; Chubu Chest Hospital; Obu Aichi-Prefecture
- Department of Bacteriology, Faculty of Medicine; Nogoya University; Nagoya
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Liu X, Geng X. A convolutional code-based sequence analysis model and its application. Int J Mol Sci 2013; 14:8393-405. [PMID: 23591850 PMCID: PMC3645750 DOI: 10.3390/ijms14048393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 03/28/2013] [Accepted: 04/10/2013] [Indexed: 11/16/2022] Open
Abstract
A new approach for encoding DNA sequences as input for DNA sequence analysis is proposed using the error correction coding theory of communication engineering. The encoder was designed as a convolutional code model whose generator matrix is designed based on the degeneracy of codons, with a codon treated in the model as an informational unit. The utility of the proposed model was demonstrated through the analysis of twelve prokaryote and nine eukaryote DNA sequences having different GC contents. Distinct differences in code distances were observed near the initiation and termination sites in the open reading frame, which provided a well-regulated characterization of the DNA sequences. Clearly distinguished period-3 features appeared in the coding regions, and the characteristic average code distances of the analyzed sequences were approximately proportional to their GC contents, particularly in the selected prokaryotic organisms, presenting the potential utility as an added taxonomic characteristic for use in studying the relationships of living organisms.
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Affiliation(s)
- Xiao Liu
- College of Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing 400044, China; E-Mail:
| | - Xiaoli Geng
- College of Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing 400044, China; E-Mail:
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Gyllenberg M, Koski T. Bayesian predictiveness, exchangeability and sufficientness in bacterial taxonomy. Math Biosci 2002; 177-178:161-84. [PMID: 11965254 DOI: 10.1016/s0025-5564(01)00096-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a theory of classification and predictive identification of bacteria. Bacterial strains are characterized by a binary vector and the taxonomy is specified by attaching a label to each vector. The theory is developed from only two basic assumptions, viz. that the sequence of pairs of feature vectors and the attached labels is judged (infinitely) exchangeable and predictively sufficient. We derive expressions for the training error and the probability of identification error and show that latter is an affine function of the former. We prove the law of large numbers for identification matrices, which contain the fundamental information of bacterial data. We prove the Bayesian risk consistency of the predictive identification rule given by the theory and show that the training error is a consistent estimate of the generalization error.
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Affiliation(s)
- Mats Gyllenberg
- Department of Mathematics, University of Turku, 20014 Turku, Finland.
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De Luca J, Ortiz Jaureguizar E, Dulout F. A multivariate approach to the association pattern of reciprocal translocations induced by chemicals and ionizing radiation in mouse germ cells. Genet Mol Biol 2000. [DOI: 10.1590/s1415-47572000000300014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The degree of similarity between chemical and physical agents in their capacity to induce reciprocal translocations was analyzed by means of multivariate analysis techniques. The effect of three different doses of gamma rays, four doses of X-rays and different doses of adriamycin, mitomycin C, thio-tepa and bleomycin was analyzed. Data were arranged in a basic matrix by two methods: cluster analysis and ordination. Two main groups were found, one including doses of 9 and 10 Gy and the other including the remaining lower doses of ionizing radiation and the other chemicals. Various subgroups were found within the second group. Accordingly, using presence/absence data there was not a specific pattern of chromosomal damage induction for physical and chemical agents. The increase in the frequencies of reciprocal translocation observed with 9 and 10 Gy was due to an increase in the kind of multivalent configurations. This variability could be dose dependent. Likewise, the similarity observed in the second group between the chemicals and the lower doses of ionizing radiation could also be dose dependent.
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Affiliation(s)
| | | | - F.N. Dulout
- Facultad de Ciencias Veterinarias, Argentina
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2 Characterization Tests for Numerical Taxonomy Studies. METHODS IN MICROBIOLOGY 1988. [DOI: 10.1016/s0580-9517(08)70408-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Kurohara SS, George FW. Objective procedure of constructing stages in cancer. Its application in recurrent carcinoma of the corpus uteri. ACTA RADIOLOGICA: THERAPY, PHYSICS, BIOLOGY 1970; 9:513-527. [PMID: 5493034 DOI: 10.3109/02841867009129127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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11
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Kiehn ED, Pacha RE. Characterization and relatedness of marine vibrios pathogenic to fish: deoxyribonucleic acid homology and base composition. J Bacteriol 1969; 100:1248-55. [PMID: 5391231 PMCID: PMC250305 DOI: 10.1128/jb.100.3.1248-1255.1969] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Deoxyribonucleic acid (DNA) isolated from several pathogenic marine vibrios was utilized in studies of base composition and nucleotide sequence relationships. Patterns of relatedness inferred from DNA criteria were found to correlate closely with those inferred from morphological, physiological, and serological analysis of the same organisms. The utility of the phenotypic and genotypic approaches to the determination of relatedness is discussed.
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Tsukamura M. Identification of group II scotochromogens and group 3 non-photochromogens of mycobacteria. TUBERCLE 1969; 50:51-60. [PMID: 5781383 DOI: 10.1016/0041-3879(69)90007-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Tsukamura M, Mizuno S. "Hypothetical mean organisms" of mycobacteria. A study of the classification of mycobacteria. JAPANESE JOURNAL OF MICROBIOLOGY 1968; 12:371-84. [PMID: 4179142 DOI: 10.1111/j.1348-0421.1968.tb00410.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Amsterdam D, Wolfe MW. Comparison of reagent-impregnated paper strips and conventional tests for distinguishing Escherichia from Aerobacter: correlation with colonial morphology. Appl Microbiol 1968; 16:1460-4. [PMID: 4879210 PMCID: PMC547684 DOI: 10.1128/am.16.10.1460-1464.1968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The means for distinguishing Escherichia from Aerobacter (Enterobacter) differ in laboratories and range from complete dependence on colonial reactions on typical gram-negative media to reliance on one or more of the classical indole, methyl red, Voges-Proskauer, citrate (IMViC) parameters. Three colonial types (one prejudged as Escherichia) of lactose-positive rods were catalogued on each of the most commonly used selective media, MacConkey Agar, Endo Agar, and E M B Agar. Each cultural type was presumptively diagnosed and then compared with the expected outcome of individual IMViC tests. The distribution of preliminary identifications was similar from growth patterns on MacConkey Agar and E M B Agar, but it differed markedly from Endo Agar. When organisms initially diagnosed by cultural methods were compared by single IMViC tests, it was found that for each colonial type one of the biochemical parameters was best suited. Thus, for those types initially considered Escherichia, the methyl red or Voges-Proskauer test results agreed most consistently; for other types, the citrate reaction was most satisfactory. In addition, when newly formulated reagent-impregnated paper strip methods for indole, Voges-Proskauer, and citrate were evaluated and compared to the standard methods, agreement was 97% for indole, 90% for Voges-Proskauer, and 95% for Simmons' citrate.
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Tsukamura M, Mizuno S, Tsukamura S. Numerical classification of atypical Mycobacteria. JAPANESE JOURNAL OF MICROBIOLOGY 1967; 11:233-41. [PMID: 5301575 DOI: 10.1111/j.1348-0421.1967.tb00341.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Abstract
Lockhart, W. R. (Iowa State University, Ames), and Karen Koenig. Use of secondary data in numerical taxonomy of the genus Erwinia. J. Bacteriol. 90:1638-1644. 1965.-Numerical methods were used to study 34 bacterial cultures, including several species of Erwinia and selected representatives of other genera of the Enterobacteriaceae. Separate computations were made by use of varying amounts of secondary data (i.e., information regarding descriptive or quantitative characters applicable only to organisms yielding a positive result in another primary character). Substantially the same groupings of the test organisms were obtained in all computations, but definition of groups seemed to be more precise when secondary data were included. The results confirm proposals by other workers that E. carotovora, E. aroideae, E. atroseptica, and E. ananas be placed in a single species, separate from E. amylovora. Limited evidence suggests that E. nimipressuralis and E. chrysanthemi may be distinct species, and that some strains of E. amylovora are not very similar either to one another or to other members of the Enterobacteriaceae.
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McCarthy BJ. The evolution of base sequences in polynucleotides. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1965; 4:129-60. [PMID: 5337874 DOI: 10.1016/s0079-6603(08)60786-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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