Academic literature on the topic 'Microbial taxonomy'
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Journal articles on the topic "Microbial taxonomy"
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Thompson, Cristiane C., Luciane Chimetto, Robert A. Edwards, Jean Swings, Erko Stackebrandt, and Fabiano L. Thompson. "Microbial genomic taxonomy." BMC Genomics 14, no. 1 (2013): 913. http://dx.doi.org/10.1186/1471-2164-14-913.
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Sanford, Robert A., Karen G. Lloyd, Konstantinos T. Konstantinidis, and Frank E. Löffler. "Microbial Taxonomy Run Amok." Trends in Microbiology 29, no. 5 (May 2021): 394–404. http://dx.doi.org/10.1016/j.tim.2020.12.010.
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Bowman, John P. "Proteomic applications in microbial identification." Microbiology Australia 32, no. 2 (2011): 77. http://dx.doi.org/10.1071/ma11077.
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Proteomics-based approaches have been used in microbial taxonomy for the last several decades. Recent improvements in instruments and software have led to the appearance of mass spectrometric fingerprinting and peptide survey approaches allowing for highly rapid and accurate taxonomic diagnoses suitable for high-throughput laboratories as well as means to deeply analyse entire proteomes.
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HÖFLING, José F., Edvaldo A. R. ROSA, Mirian J. BAPTISTA, and Denise M. P. SPOLIDÓRIO. "New Strategies on Molecular Biology Applied to Microbial Systematics." Revista do Instituto de Medicina Tropical de São Paulo 39, no. 6 (November 1997): 345–52. http://dx.doi.org/10.1590/s0036-46651997000600007.
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Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50’s and 60’s. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint
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Kapili, Bennett J., and Anne E. Dekas. "PPIT: an R package for inferring microbial taxonomy from nifH sequences." Bioinformatics 37, no. 16 (February 13, 2021): 2289–98. http://dx.doi.org/10.1093/bioinformatics/btab100.
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Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset, we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability and implementation PPIT is freely available to noncommercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online.
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Moore, Edward R. B., Sashka A. Mihaylova, Peter Vandamme, Micah I. Krichevsky, and Lenie Dijkshoorn. "Microbial systematics and taxonomy: relevance for a microbial commons." Research in Microbiology 161, no. 6 (July 2010): 430–38. http://dx.doi.org/10.1016/j.resmic.2010.05.007.
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Tamames, Javier, and Ramon Rosselló-Móra. "On the fitness of microbial taxonomy." Trends in Microbiology 20, no. 11 (November 2012): 514–16. http://dx.doi.org/10.1016/j.tim.2012.08.012.
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Green, J. L., B. J. M. Bohannan, and R. J. Whitaker. "Microbial Biogeography: From Taxonomy to Traits." Science 320, no. 5879 (May 23, 2008): 1039–43. http://dx.doi.org/10.1126/science.1153475.
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Tsai, Ming-Hsin, Yen-Yi Liu, Von-Wun Soo, and Chih-Chieh Chen. "A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy." Microorganisms 7, no. 6 (June 3, 2019): 161. http://dx.doi.org/10.3390/microorganisms7060161.
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Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.
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Chun, Jongsik, and Fred A. Rainey. "Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea." International Journal of Systematic and Evolutionary Microbiology 64, Pt_2 (February 1, 2014): 316–24. http://dx.doi.org/10.1099/ijs.0.054171-0.
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The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.
Dissertations / Theses on the topic "Microbial taxonomy"
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Mheen, Hye Sook. "Computer program for polyphasic taxonomy." Thesis, University of Newcastle Upon Tyne, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299419.
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El, Semary Nermin Adel Hussein. "Anabaena and associated bacteria : molecular approaches to studying microbial community structure and taxonomy." Thesis, University of Bristol, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420889.
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Melo, Ricardo Rodrigues de 1985. "Produção e caracterização bioquímica de uma nova transglutaminase microbiana = Production and biochemical characterization of a new microbial transglutaminase." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/254360.
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Orientador: Hélia Harumi SatoDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos
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Resumo: Transglutaminase é uma enzima capaz de catalisar a formação de ligações cruzadas intra- e intermoleculares entre proteínas, peptídeos e aminas primárias por meio de ligações covalentes entre resíduos de lisina e glutamina. Desta forma, transglutaminase pode ser utilizada em diversos setores industriais para o desenvolvimento de novos produtos ou para a modificação de suas características. A linhagem B6 isolada de amostra de solo coletada na região do Estado de Minas Gerais foi identificada como tendo características morfológicas típicas de actinomicetos e pela análise da região 16S rRNA há colocou na subclasse Streptomyces próximo a linhagem Streptomyces angustmycinicus NBRC 3934T. A fim de aumentar a produção de transglutaminase (2,75 U/mL) pela linhagem Streptomyces sp. B6, o meio de fermentação foi submetido a processos de otimização. Como primeiro passo da otimização, o crescimento do micro-organismo e a produção da enzima foram estudados através de uma pré-seleção de fontes de carbono, nitrogênio e sais no meio de produção. Após as análises das diferentes fontes, um delineamento experimental do tipo Plackett-Burman foi utilizado para a seleção dos componentes do meio de cultivo que afetam a produção de transglutaminase. Os resultados do delineamento experimental indicaram que a produção de transglutaminase foi influenciada negativamente pela peptona bacteriológica e MgSO4.7H2O, positivamente pelo amido de batata, glicose, peptona de caseína e KH2PO4.7H2O e não foi influenciada pelo farelo de soja, considerando um nível de confiança de 95%. A concentração de amido de batata foi fixada no maior nível testado no planejamento Plackett-Burman devido à gelificação do meio de fermentação em concentrações maiores. Assim, os três fatores que influenciaram a produção de transglutaminase (glicose, peptona de caseína e KH2PO4.7H2O) foram otimizados para obter o máximo de produção da enzima utilizando delineamento composto central. Sob a condição otimizada, a qual continha 25 g/L de farinha de soja, 35 g/L de amido de batata, 5 g/L de glicose, 24,5 g/L de peptona de caseína e 8 g/L de KH2PO4.7H2O, a atividade enzimática atingiu 6,13 U/mL, apresentando 125% à mais de atividade em relação á obtida no meio antes da otimização. A transglutaminase microbiana produzida pela linhagem Streptomyces sp. B6 exibiu atividade ótima em 45°C e em pH de 6,5 e 11,0. A enzima manteve-se estável na faixa de pH 3,0-11,0 durante 60 minutos à 40°C durante 3 horas. A transglutaminase não foi inibida por Ca2+, Na+, Co2+, Mn2+, K+, Mg2+, Ba2+, EDTA, L-cisteína e glutationa na concentração de 5 mM, mas foi inibida na presença de Hg2+, Cu2+, Zn2+ e Fe2+ na concentração de 5mM. A linhagem Streptomyces sp. B6 é uma nova fonte de transglutaminase com características interessantes para aplicações biotecnológicas
Abstract: Transglutaminase is an enzyme capable of catalyzing the forming intra-and intermolecular cross-linking between proteins, peptides and primary amines by covalent bonds between lysine and glutamine residues. Thus, transglutaminase can be used in food processing industries to develop new products and modify their characteristics. The B6 strain was isolated from soil sample collected in the region state of Minas Gerais was identified as having morphological characteristics typical of the actinomycetes, and the 16S rRNA analysis placed it in the Streptomyces subclade, closely related to Streptomyces angustmycinicus NBRC 3934T. In order to increase the transglutaminase production (2.75 U/mL) from Streptomyces sp. B6 strain, the fermentation medium was subjected to optimization processes. In the first step of optimization, the micro-organism growth and enzyme production were studied through a pre-selection of carbon, nitrogen and salts sources in the culture medium. After analysis of different sources, the Plackett¿Burman experimental design was used for screening the components of the culture medium that affect the transglutaminase production. Results of the experiment indicated that production of transglutaminase was negatively influenced by bacteriological peptone and MgSO4.7H2O, positively influenced by potato starch, glucose, casein peptone and KH2PO4.7H2O and was not influenced by soybean meal, considering 95% of confidence level. The potato starch concentration was fixed at the highest level tested in Plackett¿Burman design due to gelation of the fermentation medium in higher concentrations. Thus, the three factors that influence the transglutaminase production (glucose, casein peptone and KH2PO4.7H2O concentrations) were optimized to obtain the maximum transglutaminase production using central composite design. Under the proposed optimized condition, which contained 25 g/L soybean meal, 35 g/L potato starch, 5 g/L glucose, 24.5 g/L casein peptone and 8 g/L KH2PO4.7H2O, the enzyme activity reached 6.13 U/mL, which was 125% more than the activity in relative obtained medium before optimization. The microbial transglutaminase produced by Streptomyces sp. B6 strain exhibited optimal activity at 45 oC and at pH 6.5 and 11.0. The enzyme remained stable in the pH range from 3.0 - 11.0 for 60 minutes and at 40 oC temperature for 3 hours. The transglutaminase was not inhibited by Ca2+, Na+, Co2+, Mn2+, K+, Mg2+, Ba2+, EDTA, L-cysteine and glutathione in concentration 5 mM, but was inhibited in the presence of Hg2+, Cu2+, Zn2+ and Fe2+ in concentration 5 mM. In conclusion, Streptomyces sp. B6 strain is a new source of transglutaminase with interesting features for biotechnological applications
Mestrado
Ciência de Alimentos
Mestre em Ciência de Alimentos
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Buckley, Elan. "Change in the Structure of Soil Microbial Communities in Response to Waste Amendments." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/101499.
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Soil microbial communities are affected extensively by addition of amendments to their environment. Of particular concern is the addition of poultry litter, which contains a substantial C, energy, and nutrient supply, but also antibiotic resistance genes (ARG), antimicrobials, and a multitude of microbial species. This project seeks to primarily assess if there is a change in bacterial community structure in response to poultry litter amendments to pasture land across geographically independent land across northern Georgia. It may be that changes in the relative abundance of bacterial communities also result in alteration in ARGs, and the community resistance to antibiotics (“resistome”) which in turn increases the potential threat of antibiotic resistance genes. While another part of this study will determine changes in integrons and specific ARGs, this project will focus on changes in bacterial communities and the potential functional changes in the community, which in turn have consequences for ARG levels and its horizontal transfer to various members of the soil community. Addition of waste from livestock is a historical method for increasing nutrients needed in the soil for the cultivation of crops, and in turn causes pronounced shifts in soil microbial communities due to the addition of large amounts of carbon, nutrients, foreign microbes, and other material. This study is unique because it utilizes a novel and relatively large landscape-scale to determine if there are discernable and repeatable patterns of bacterial community structure change in response to amendment regardless of exact soil type or source of chicken litter amendment. In the future, these data can also provide insight into the changes in the relative abundance antibiotic related genes associated with community change.M.S.
Soil is complicated, both in terms of its physical makeup and the organisms that live inside of it. Predicting changes in soil based on the addition of foreign material such as chemicals or biological waste is not an easy process, and whether or not it is even possible to reliably predict those changes is a matter of some dispute. This study is designed to illustrate that such changes can in fact be reliably and consistently predicted even with regard to the addition of complicated materials to the soil. In this study, specifically, the material in question is chicken litter. A mix of the bedding and waste produced by chickens, litter is commonly handled by composting and is added to soil in farms as a fertilizer rich in organic matter. It is possible to point at specific elements of the soil such as the chemistry and bacteria and see how it is changed with the addition of chicken litter, which allows us to determine the nature and extent of the change that chicken litter has on soil. This study is conducted on a larger scale than similar experiments conducted in the past, making it apparent that these relationships exist on a repeated basis. It is the object of this study to pave the way and make it easier for scientists in the future to determine these relationships in other unique contexts.
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Blank, Carrine E., Hong Cui, Lisa R. Moore, and Ramona L. Walls. "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions." BIOMED CENTRAL LTD, 2016. http://hdl.handle.net/10150/614758.
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Background: MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. Results: MicrO currently has similar to 14550 classes (similar to 2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by similar to 24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. Conclusions: By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we intend MicrO to be a powerful new tool to increase the computing power of bioinformatics tools such as the automated text mining of prokaryotic taxonomic descriptions using natural language processing. We also intend MicrO to support the development of new bioinformatics tools that aim to develop new connections between microbial phenotypes and genotypes (i.e., the gene content in genomes). Future ontology development will include incorporation of pathogenic phenotypes and prokaryotic habitats.
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Shahrivar, Damon. "Accurate and fast taxonomic profiling of microbial communities." Thesis, KTH, Kommunikationsteori, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-162919.
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With the advent of next generation sequencing there has been an explosion of the size of data that needs to be processed, where next generation sequencing yields basepairs of DNA in the millions. The rate at which the size of data increases supersedes Moores law therefore there is a huge demand for methods to nd meaningful labels of sequenced data. Studies of microbial diversity of a sample is one such challenge in the eld of metagenomics. Finding the distribution of a bacterial community has many uses for example, obesity control. Existing methods often resort to read-by-read classication which can take several days of computing time in a regular desktop environment, excluding genomic scientists without access to huge clusters of computational units. By using sparsity enforcing methods from the general sparse signal processing eld (such as compressed sensing), solutions have been found to the bacterial community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. The inference task is reduced to a general statistical model based on kernel density estimation techniques that are solved by existing convex optimization tools. The objective is to o er a reasonably fast community composition estimation method. This report proposes, clustering as a means of aggregating data to improve existing techniques run-time and biological delity. Use of convex optimization tools to increase the accuracy of mixture model parameters are also explored and tested. The work is concluded by experimentation on proposed improvements with satisfactory results. The use of Dirichlet mixtures is explored as a parametric model of the sample distribution where it is deemed that the Dirichlet is a good choice for aggregation of k-mer feature vectors but the use of Expectation Maximization is unt for parameter estimation of bacterial 16s rRNA samples. Finally, a semi-supervised learning method found on distance based classication of taxa has been implemented and tested on real biological data with high biological delity.Nya tekniker inom DNA-sekvensering har givit upphov till en explosion pa data som nns att tillga. Nasta generations DNA-sekvensering generar baspar som stracker sig i miljonerna och mangden data okas i en exponentiell takt, vilket ar varfor det nns ett stort behov av ny skalbar metodik som kan analysera kvantitiv data for att fa ut relevant information. Den bakteriella artfordelning av ett provror ar en sadan problemst allning inom meta-genomik, vilket har era tillampningsomraden som exempelvis, studier av fettma. I dagslaget sa ar den vanligaste metoden for att fa ut artfordelningen genom att klassiera DNA-strangarna av bakterierna, vilket ar en tidskravande losning som kan ta upp emot ett dygn for att processera data med hog upplosning. En snabb och tillforlitlig losning skulle darfor tillata er forskare att ta del av nasta generations sekvensering och analysera dess data som i sin tur skulle ge upphov till mer innovation inom omradet. Alternativa losningar med inspiration fran signalbehandlig har hittats som nyttjar problemestallningens glesa natur genom anvandning av Compressed Sensing. Svar hittas genom att simultant tilldela strangar till en for-processerad referensdatabas. Problemstallningen har forenklats till en statistisk modell av provror med ickeparametrisk estimering for att implicit fa ut fordelningen av bakteriearter med hjalp av konvex optimering. Denna rapport foreslar anvandningen av klustrering for aggregering av data for att forbattra tillforlitligheten av svaren och minska tiden for berakning av dessa. Anvandningen av parametriska modeller, Dirichlet fordelningen, har utforskats dar rapporten har kommit fram till att antaganden for lampligheten av denna som ett medel att aggregera k-mer vektorer ~Ar rimliga men att parameterestimeringen med Expectation Maximization ej fungerar val i samband med Dirichlet och en omskrivning av parametern skulle behovas i vektorrymden som spans av 16S rRNA genen. Slutligen sa har distansbaserad tilldelning av bakterier testats pa data fran verklig biologisk kontext med valdigt hog noggranhet. ii
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Toczydlowski, David G. "Aquatic microbial community responses to stress: comparison of nontaxonomic and taxonomic indices." Thesis, Virginia Tech, 1985. http://hdl.handle.net/10919/45672.
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Three nontaxonomic indices; ATP/Chlorophyll a(ATP/Chla),
ATP/ADP, and Chlorophyll a/Pheopigment (Chla/Pheo) were compared
to the taxonomic measures of species diversity (d) and species
richness as indicators of stress in aquatic environments. Field
and laboratory microcosm responses of indigenous microbial
communities exposed to municipal sewage treatment plant (STP)
effluent were monitored. The STP effluent produced increased
adenylate concentrations, ATP/ADP and ATP/Chla ratios, and
decreased Chla, Chla/Pheo, d, and species richness relative to
upstream reference communities. Nontaxonomic responses were
consistent in four separate field tests.
Significant differences in responses were discernible in 3 d when communities were transferred from reference to polluted sites. Chla/Pheo decreased more rapidly than other measurements. The predictive capability of laboratory flowâ through microcosm tests was examined by simultaneously transferring communities from upstream reference sites to downstream field sites and to various dilutions of field effluent in the laboratory.
Master of Science
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Macedo, Juliana Alves 1982. "Produção, purificação, caracterização e aplicação de transglutaminase de Streptomyces sp. CBMAI 837." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/254362.
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Orientadores: Helia Harumi Sato , Lara Durães SetteTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos
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Resumo: A transglutaminase (TGase) (EC 2.3.2.13; proteina-glutamina ?-glutaminiltransferase) é uma enzima capaz de catalisar reações de transferência de grupos acil utilizando resíduos de glutamina das ligações peptídicas de proteínas como doadores de grupos acil, e diversas aminas primárias como receptores. As ligações covalentes cruzadas entre inúmeras proteínas e peptídeos pela transglutaminase promovem mudanças nas propriedades de proteínas de alimentos. Por essa razão, a transglutaminase é amplamente utilizada nas indústrias de processamento de alimentos para o desenvolvimento de novos produtos e modificação de características como: viscosidade, capacidade emulsificante e valores nutricionais. Uma cepa de Actinomyceto, isolada de amostras de solo brasileiro, foi investigada taxonomicamente por uma combinação de técnicas moleculares e morfológicas, resultando na conclusão de que a cepa pertence ao gênero Streptomyces sp. A cepa, chamada de Streptomyces sp. CBMAI 837 produziu transglutaminase quando cultivada a 30°C por cinco dias, em agitador rotatório, no meio de fermentação otimizado, composto por: 0,2% KH2PO4, 0,1% MgSO4.7H2O, 2% farinha de soja, 2% amido de batata, 0,2% glicose, e 2% peptona, atingindo uma atividade enzimática de 1,37 U.mL-1. A transglutaminase foi purificada cerca de 5 vezes através de duas passagens cromatográficas sucessivas em uma coluna de filtração em gel Sephadex G-75, com 17% de recuperação. A purificação da proteína foi comprovada por homogeneidade eletroforética em SDS-PAGE. A massa molar da TGase foi estimada em cerca de 45 kDa. A transglutaminase de Streptomyces sp CBMAI 837, tanto na forma bruta quanto purificada, apresentou atividade enzimática ótima em pH 6,0-6,5, e em 35-40°C. Um segundo pico de atividade ótima foi observado em pH 10,0 na enzima no estado bruto. Ambas as formas da enzima foram estáveis na faixa de pH de 4,5 a 8,0 e até 45°C. A transglutaminase na forma bruta e purificada mostrou-se independente de íons cálcio, mas foi ativada na presença de K+, Ba2+, e Co2+; e inibida por Cu2+ e Hg2; o que sugere a presença de um grupo tiol no sítio ativo da enzima. A TGase purificada apresentou um Km de 6,37 mM e um Vmax de 1,70 U/mL, enquanto a enzima bruta apresentou Km de 6,52 mM e um Vmax de 1,35 U/mL para o substrato N-carbobenzoxi-L-glutaminil-glicina. A influência da transglutaminase de Streptomyces sp CBMAI 837 bruta, nas propriedades de géis ácidos de caseinato de sódio foi investigada, tendo como parâmetro géis preparados com a TGase comercial (Ajinomoto Inc.). Os géis com a enzima comercial tiveram um valor de módulo de elasticidade maior, porém, dependendo da concentração de proteína, estes foram menos deformáveis. Os géis com enzima bruta de Streptomyces sp. CBMAI 837 se mostraram muito mais rígidos e menos elásticos. Resultados da eletroforese indicaram que a enzima comercial promoveu a formação de polímeros de proteínas de massa molecular mais alta do que a enzima de Streptomyces sp. CBMAI 837. Os testes de microscopia eletrônica de varredura e da capacidade de retenção de água mostraram que características particulares de cada um dos géis poderiam estar associadas ao tipo específico de interação promovida por cada uma das amostras enzimáticas testadas
Abstract: Transglutaminase (EC 2.3.2.13; protein-glutamine ?-glutaminyltransferase) is an enzyme that catalysis an acyl transfer reaction using protein or peptide-bond glutamine residues as acyl donors and several primary amines as receptors. The covalent cross-links between a number of proteins and peptides introduced by transglutaminase promote modification of the functional properties of the food proteins. Therefore, transglutaminase are widely used by food-processing industries for the purpose of new product development, modification of the product properties such as viscosity, emulsification foaming and nutritional values. An actinomycete strain, isolated from Brazilian soil, was taxonomically investigated using a combination of molecular and morphological basedmethods, resulting on the conclusion that the strain belongs to the genus Streptomyces sp. The strain, named Streptomyces sp. CBMAI 837, produce transglutaminase when cultivated at 30°C for 5 days at 200 rpm in a rotatory shaker, on the optimized fermentation medium composed of 0.2% KH2PO4, 0.1% MgSO4.7H2O, 2% soybean flour, 2% potato starch, 0.2% glucose, and 2% peptone, with a enzymatic activity of 1.37 U.mL-1. The enzyme purification was performed by of two successive chromatographies on Sephadex G-75 columns with yields of 48% and 17%, respectively. The protein purification was successfully achieved to electrophoretical homogeneity on SDS-PAGE. The molecular mass of the MTGase was estimated to be about 45 kDa. The enzyme from Streptomyces sp., in both crude and pure forms, exhibited optimal activity in the 6.0-6.5 pH range and at 35-40°C. A second maximum of activity was observed at pH 10.0 on the crude Streptomyces sp. enzyme. Both forms of transglutaminase were stable over the pH range from 4.5 to 8.0 and up to 45°C. The activities of all the TGase samples were independent of Ca+2 concentration, but they were elevated in the presence of K+, Ba2+, and Co2+ and inhibited by Cu2+ and Hg2+, which suggests the presence of a thiol group in the TGase¿s active site. The purified enzyme presented Km of 6.37 mM and Vmax of 1.7 U/mL, while the crude enzyme demonstrated Km of 6.52 mM and Vmax of 1.35 U/mL. The influence of the transglutaminase on acid-gel properties was studied. Texture parameters showed that the commercial TGase (Ajinomoto Inc.) gels had greater values of elasticity modulus and could promote the formation of more elastic and soft food systems, while addition of the crude TGase of Streptomyces sp. CBMAI 837 to the gel led to the formation of more rigid and less elastic gels. The electrophoresis showed that the commercial TG enzyme in this system promoted higher molecular mass protein polymers than the enzyme from Streptomyces sp. CBMAI 837. Microscopy and water holding capacity (WHC) observations showed that all the gel characteristics could be associated to specific interactions promoted by each TGase tested
Doutorado
Doutor em Ciência de Alimentos
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Dayo-Owoyemi, Ifeloju [UNESP]. "Taxonomic assessment and biotechnological potential of yeasts hold at the Unesp - Central for microbial resources." Universidade Estadual Paulista (UNESP), 2013. http://hdl.handle.net/11449/103973.
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dayoowoyemi_i_dr_rcla.pdf: 2213436 bytes, checksum: 57ef54bb4924dae1b326ff6c146c0802 (MD5)Atualmente, existe um crescente interesse em explorar diversos habitats, a fim de revelar a biodiversidade microbiana, incluindo as leveduras. Tal diversidade ainda não acessada guarda a descoberta de novas espécies para ciência, provavelmente muitas das quais com potencial para aproveitamento em processos biotecnológicos. Com o objetivo de explorar e conservar a diversidade de fungos, o Central de Recursos Microbianos da UNESP (CRM – UNESP) mantém em seu acervo várias estirpes de leveduras isoladas de ecossistemas diversos, sendo alguns deles pouco explorados. No início deste trabalho sabíamos que muitas das leveduras depositadas no acervo do CRM – UNESP não estavam totalmente caracterizadas tanto em nível taxonômico, quanto em relação ao potencial biotecnológico que poderiam apresentar. Portanto, o presente estudo foi desenhado para caracterizar e identificar taxonomicamente leveduras depositadas no CRM – UNESP, bem como selecionar estirpes que produzem enzimas extracelulares degradadoras de polissacarídeos como amilase, celulase, xilanase, pectinase e ligninase. Usando uma abordagem polifásica, um total de 340 isolados de leveduras foi identificado, sendo que 71,2% compreendem 43 taxa de ascomicetos e os restantes 28,8% foram classificados em 27 taxa de basidiomicetos. O estudo também levou à descoberta de 8 prováveis novas espécies. Baseado nesta constatação, a classificação taxonômica e análise filogenética foi realizada para duas espécies anamórficas de ascomicetos e uma espécie teleomórfica de basidiomiceto. A descrição destas três espécies é apresentada neste estudo. Os resultados demonstraram que Wickerhamiella kiyanii FB1-1DASPT e W. pindamonhangabaensis H10YT pertencem à clade Wickerhamiella da ordem Saccharomycetales...
In recent time, there has been an increasing interest in exploring diverse ecological habitats in order to reveal the yeast biodiversity. The increased awareness in the biotechnological potentials of yeasts has also spurred attempts to search for new species with novel biotechnological capabilities. Aiming to explore and conserve the fungal diversity from various ecosystems, the UNESP – Central for Microbial Resources (UNESP – CMR) harbors various strains of ecologically diverse yeasts isolates, some of which were yet to be identified. Therefore, this study was designed to identify and characterize some yeasts from the UNESP – MRC and to select strains possessing extracellular plant polysaccharide degrading enzymes namely amylase, cellulase, xylanase, pectinase and ligninase. Using a polyphasic approach, a total of 340 strains were identified. Taxonomic classification grouped 71.2% of these isolates into 43 ascomycetous taxa while the remaining 28.8% were classified in 27 basidiomycetous taxa. The study also led to the discovery of 8 putative new species. As a result, we classified two anamorphic species in the Ascomycota and one teleomorphic species in the Basidiomycota. In this study we provide the description of both species. Our results demonstrated that the two ascomycetous species proposed as Wickerhamiella kiyanii FB1-1DASPT and W. pindamonhangabaensis H10YT belong to the Wickerhamiella clade of the Saccharomycetales (Saccharomycetes) while the basidiomycetous species proposed as Bulleromyces texanaensis ATT064T belong to the Bulleromyces / Papiliotrema / Auriculibuller clade of the Tremellales (Agaricomycotina). In order to show the significance of intraspecific diversity in yeasts, in one of our studies, we subjected 11 strains, (including the type strain CBS 8960T) of Hannaella kunmingensis... (Complete abstract click electronic access below)
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Dayo-Owoyemi, Ifeloju. "Taxonomic assessment and biotechnological potential of yeasts hold at the Unesp - Central for microbial resources /." Rio Claro, 2012. http://hdl.handle.net/11449/103973.
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Orientador: Fernando Carlos PagnoccaCoorientador: André Rodrigues
Banca: Lara Durães Sette
Banca: Vanderlei Gerlado Martins
Banca: Paula Benevides de Morais
Banca: Aline Silva
Resumo: Atualmente, existe um crescente interesse em explorar diversos habitats, a fim de revelar a biodiversidade microbiana, incluindo as leveduras. Tal diversidade ainda não acessada guarda a descoberta de novas espécies para ciência, provavelmente muitas das quais com potencial para aproveitamento em processos biotecnológicos. Com o objetivo de explorar e conservar a diversidade de fungos, o Central de Recursos Microbianos da UNESP (CRM - UNESP) mantém em seu acervo várias estirpes de leveduras isoladas de ecossistemas diversos, sendo alguns deles pouco explorados. No início deste trabalho sabíamos que muitas das leveduras depositadas no acervo do CRM - UNESP não estavam totalmente caracterizadas tanto em nível taxonômico, quanto em relação ao potencial biotecnológico que poderiam apresentar. Portanto, o presente estudo foi desenhado para caracterizar e identificar taxonomicamente leveduras depositadas no CRM - UNESP, bem como selecionar estirpes que produzem enzimas extracelulares degradadoras de polissacarídeos como amilase, celulase, xilanase, pectinase e ligninase. Usando uma abordagem polifásica, um total de 340 isolados de leveduras foi identificado, sendo que 71,2% compreendem 43 taxa de ascomicetos e os restantes 28,8% foram classificados em 27 taxa de basidiomicetos. O estudo também levou à descoberta de 8 prováveis novas espécies. Baseado nesta constatação, a classificação taxonômica e análise filogenética foi realizada para duas espécies anamórficas de ascomicetos e uma espécie teleomórfica de basidiomiceto. A descrição destas três espécies é apresentada neste estudo. Os resultados demonstraram que Wickerhamiella kiyanii FB1-1DASPT e W. pindamonhangabaensis H10YT pertencem à clade Wickerhamiella da ordem Saccharomycetales... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: In recent time, there has been an increasing interest in exploring diverse ecological habitats in order to reveal the yeast biodiversity. The increased awareness in the biotechnological potentials of yeasts has also spurred attempts to search for new species with novel biotechnological capabilities. Aiming to explore and conserve the fungal diversity from various ecosystems, the UNESP - Central for Microbial Resources (UNESP - CMR) harbors various strains of ecologically diverse yeasts isolates, some of which were yet to be identified. Therefore, this study was designed to identify and characterize some yeasts from the UNESP - MRC and to select strains possessing extracellular plant polysaccharide degrading enzymes namely amylase, cellulase, xylanase, pectinase and ligninase. Using a polyphasic approach, a total of 340 strains were identified. Taxonomic classification grouped 71.2% of these isolates into 43 ascomycetous taxa while the remaining 28.8% were classified in 27 basidiomycetous taxa. The study also led to the discovery of 8 putative new species. As a result, we classified two anamorphic species in the Ascomycota and one teleomorphic species in the Basidiomycota. In this study we provide the description of both species. Our results demonstrated that the two ascomycetous species proposed as Wickerhamiella kiyanii FB1-1DASPT and W. pindamonhangabaensis H10YT belong to the Wickerhamiella clade of the Saccharomycetales (Saccharomycetes) while the basidiomycetous species proposed as Bulleromyces texanaensis ATT064T belong to the Bulleromyces / Papiliotrema / Auriculibuller clade of the Tremellales (Agaricomycotina). In order to show the significance of intraspecific diversity in yeasts, in one of our studies, we subjected 11 strains, (including the type strain CBS 8960T) of Hannaella kunmingensis... (Complete abstract click electronic access below)
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Books on the topic "Microbial taxonomy"
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Chowdhury, A. On taxonomy and ecology of earthworms (Annelida: Oligochaeta) from uncultivated and waste disposal sites of West Bengal with some notes on their microbial association. Kolkata: Zoological Survey of India, 2011.
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Rekadwad, Bhagwan. Microbial Systematics: Taxonomy, Microbial Ecology, Diversity. Taylor & Francis Group, 2020.
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Rekadwad, Bhagwan. Microbial Systematics: Taxonomy, Microbial Ecology, Diversity. Taylor & Francis Group, 2020.
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Rekadwad, Bhagwan. Microbial Systematics: Taxonomy, Microbial Ecology, Diversity. Taylor & Francis Group, 2020.
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Rekadwad, Bhagwan. Microbial Systematics: Taxonomy, Microbial Ecology, Diversity. Taylor & Francis Group, 2020.
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Microbial Systematics: Taxonomy, Microbial Ecology, Diversity. Taylor & Francis Group, 2022.
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Lactic Acid Bacteria Biodiversity and Taxonomy. Wiley-Blackwell, 2013.
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Godbole, Suchitra, and Dhara P. Sachdev. Basic Concepts and Recent Advances in Microbial Diversity, Taxonomy, Speciation and Evolution. Cambridge Scholars Publishing, 2024.
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NA. Microbio with Diseases Taxonomy& Microbio Pk. Addison Wesley Publishing Company, 2007.
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NA. Microbio with Diseases Taxonomy& Microbio Pk. Addison Wesley Publishing Company, 2007.
Find full textBook chapters on the topic "Microbial taxonomy"
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Thompson, Cristiane C., Livia Vidal, Vinicius Salazar, Jean Swings, and Fabiano L. Thompson. "Microbial Genomic Taxonomy." In Trends in the systematics of bacteria and fungi, 168–78. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0168.
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Abstract This book chapter argues for an open-access catalogue of taxonomic descriptions with prototypes; diagnostic tables; and links to culture collections, to genome and gene sequences, and to other phenotypic and ecological databases. Ideally, the open access taxonomy will be based solely on genome sequences that allow both the phylogenetic allocation of new strains and species in the taxonomic space and the phenotypic/metabolic characterization in open online databases. Careful and thorough annotation of the genome sequences for function and chemotaxonomic data will be required. An alternative Code will be required for the naming strategy of genomes. Current microbial taxonomy is not able to keep up with the pace of development in microbial ecology. Innovative ways of developing microbial taxonomy are, therefore, needed urgently. This novel approach can, for the first time, allow microbial species descriptions using genomes based on ecological and evolutionary theory. One challenge ahead is to leverage the use of genome sequences to obtain insights on the (in silico) phenotypes and ecology of novel taxa.
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Kristjansson, Jakob K., Gudmundur O. Hreggvidsson, and William D. Grant. "Taxonomy of Extremophiles." In Applied Microbial Systematics, 231–91. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4020-1_9.
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Semikhatov, Mikail A., and Maria E. Raaben. "Proterozoic Stromatolite Taxonomy and Biostratigraphy." In Microbial Sediments, 295–306. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-662-04036-2_32.
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Rudramurthy, Shivaprakash M., and Harsimran Kaur. "Taxonomy and Classification of Fungi." In Microbial Zoonoses, 3–19. Singapore: Springer Nature Singapore, 2024. http://dx.doi.org/10.1007/978-981-97-3214-2_1.
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Hofbauer, Wolfgang Karl, and Georg Gärtner. "Aerophytic Organisms Colonizing Façades: Diversity, Taxonomy and Ecophysiology." In Microbial life on Façades, 29–191. Berlin, Heidelberg: Springer Berlin Heidelberg, 2021. http://dx.doi.org/10.1007/978-3-662-54833-2_3.
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Ward, Alan C., and Michael Goodfellow. "Phylogeny and Functionality: Taxonomy as a Roadmap to Genes." In Microbial Diversity and Bioprospecting, 288–313. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555817770.ch28.
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Rai, Anusha, Indu, N. Smita, G. Deepshikha, K. Gaurav, K. Dhanesh, G. Suresh, Ch Sasikala, and Ch V. Ramana. "Emerging Concepts in Bacterial Taxonomy." In Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications, 3–22. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8315-1_1.
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Muhammad, Murad, Bhagwan Narayan Rekadwad, Tayyiba Habib, Lei Dong, Wael N. Hozzein, and Wen-Jun Li. "Applications of Bioactive Compounds from Novel Microbial Taxa." In Modern Taxonomy of Bacteria and Archaea, 195–208. Singapore: Springer Nature Singapore, 2024. http://dx.doi.org/10.1007/978-981-99-5720-0_10.
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Salam, Nimaichand, Shuai Li, and Wen-Jun Li. "Minimal Taxonomic Standards for Declaration of New Microbial Species." In Modern Taxonomy of Bacteria and Archaea, 1–12. Singapore: Springer Nature Singapore, 2024. http://dx.doi.org/10.1007/978-981-99-5720-0_1.
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Kale, Varsha, Lorna Richardson, and Robert D. Finn. "Navigating bacterial taxonomy in a world of unchartered microbial organisms." In Trends in the systematics of bacteria and fungi, 179–97. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0179.
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Abstract This book chapter focuses on state-of-the-art informatics techniques that perform bacterial taxonomic assertions on metabarcoding data sets and MAGs, as well as highlighting some of the advantages and disadvantages of the respective approaches and finishes by exploring why they are yet to be perfectly complementary. Currently, the results of these two approaches can be difficult to compare for the various reasons we highlight, and they are compounded by the fact that the data sets typically have different purposes. Despite the current difficulties, the field is heading in a direction that attempts to harmonize bacterial taxonomy generated by both approaches, ultimately making these comparisons less problematic in the future.
Conference papers on the topic "Microbial taxonomy"
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Abhishek, S., Anjali T, Prathibha Prakash, and Rina Barouch Bentov. "Microbial Taxonomy: An Artful Exploration of Microbes with Neural Networks." In 2023 International Conference on Intelligent Computing, Communication & Convergence (ICI3C), 365–70. IEEE, 2023. http://dx.doi.org/10.1109/ici3c60830.2023.00076.
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Enzien, Michael, Sadie Starustka, Michael Gurecki, Trinity Fincher-Miller, Bryce Kuhn, Carly Sowecke, Kody Jones, Kevin O'Sullivan, Kyle Norris, and Jason Stidham. "Metagenomics Microbial Characterization of Production and Process Fluids in the Powder River Basin: Identification and Sources of Problematic Microorganisms Associated with SWD Facilities." In SPE International Conference on Oilfield Chemistry. SPE, 2021. http://dx.doi.org/10.2118/204335-ms.
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Abstract Inconsistent bacterial control and monitoring led to variability in Salt Water Disposal (SWD) well performance and injectivity creating excess costs in biocide applications and remedial work. A metagenomics study using Whole Genome Sequencing (WGS) was conducted to determine the source(s) of problematic microorganisms throughout the process life cycle: Freshwater> Drilling> Completion> Flowback> Produced water> SWD. A total of 30 metagenomes were collected from the 6 process stages and identification and quantification of the major microbial taxa from each of these stages were identified. "Taxonomy to Function" associations were identified for all the major taxa found in the SWD fluids. WGS was performed on positive Sulfate Reducing Bacteria (SRB) and Acid Producing Bacteria (APB) media bottles inoculated in the field for a Flowback sample. Four of the six major taxa found in SWD samples are considered groups of microorganisms known to cause microbiologically influenced corrosion (MIC): Clostridia, methanogens, SRB and Iron Reducing bacteria. Thermovirga and Thermotagae, were the two most abundant taxa found in SWD samples, both thermophilic halophilic fermenting bacteria. The Fe reducing bacteria Shewanella was only detected in Drilling and SWD fluids suggesting its source was Drilling fluids. Completion fluid metagenome profiles from two separate sites followed similar patterns. During middle of completions Proteobacteria phyla were dominant taxa represented mostly by Pseudomonas. Other abundant phyla were all characteristic of polymer degrading bacteria. None of these taxa were dominant populations identified in SWD waters. Fresh water only shared similar taxa with Drilling and Completion fluids. A few minor taxa from Drilling and Completion stages show up as significant taxa in SWD fluids. The majority of taxa found in SWD samples appear to originate from Flowback and Produced waters, although at lower abundances than found in SWD samples. It cannot be determined if the microorganisms found in Flowback and Produced waters were endemic to the formation or come from contaminated source waters, i.e. process equipment used to store and transport water sources. Petrotoga mobilis was the dominant population of bacteria that grew in both media bottles, 96% and 77% for SRB and APB, respectively, while Petrotoga was detected at 14% in the field sample. The most abundant bacteria detected in field sample were Clostridia (38%) while only 2.7% were detected in APB media. SRB media bottle had 0.18% SRB detected by WGS; APB media had 9% SRB population abundance. No SRB were detected in corresponding field sample or below detectable limits (BDL) for WGS methods (<0.01%). WGS was forensically used to successfully identify type and source of problematic microorganism in SWD facilities. Results from media bottle and field sample comparisons stress the importance of developing improved field monitoring techniques that more accurately detect the dominant microorganisms.
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Egovtseva, A. Yu, T. N. Melnichuk, and S. F. Abdurashitov. "The influence of farming systems and microbial preparations on the structure of the microbocenosis of the rhizosphere of Triticum aestivum L." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.063.
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The use of microbial preparations contributed to a change in the taxonomic structure of winter wheat rhizosphere microbiome was established. A more significant effect of microbial preparations was noted under no-till technology on the structure of the microbiome than with the traditional farming system.
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Muratova, A. Yu, A. A. Nurzhanova, and O. V. Turkovskaya. "Effect of heavy metals and hydrocarbons on rhizosphere microbial communities of Miscanthus × giganteus." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.178.
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Microbiological analysis of soil from the root zone of Miscanthus × giganteus revealed differences in the physiological and taxonomic structure of the rhizosphere microbial community under the influence of soil contamination with zinc and oil sludge.
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Pyliak, Nina, and Basil Khodorchuk. "The biotechnological potential of microorganisms determination for creating complex preparations with insect-fungicidal properties." In Scientific International Symposium "Plant Protection – Achievements and Perspectives". Institute of Genetics, Physiology and Plant Protection, Republic of Moldova, 2023. http://dx.doi.org/10.53040/ppap2023.29.
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The research results of the biotechnological potential of microbial strains with different taxonomic statuses are presented for stable microbial consortia creation in complex preparations with insect-fungicidal properties development. Six strains of microorganisms with fungicidal properties and four with insecticidal properties were selected from the Collection of the Engineering and Technological Institute "Biotekhnika" of the National Academy of Agrarian Sciences of Ukraine. Their biotechnological potential was analyzed toward test objects (phytopathogens and insects). It was found that Trichoderma fungi demonstrate the highest fungicidal activity, while Streptomyces fungi exhibit the highest insecticidal activity.
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Forona, B., S. Ramakrishnan, V. Keerthieswar, S. Sowmiya, S. Swetha, and K. Ram. "Taxonomic and functional metagenomic profiling of microbial communities in urine sample." In THE 8TH ANNUAL INTERNATIONAL SEMINAR ON TRENDS IN SCIENCE AND SCIENCE EDUCATION (AISTSSE) 2021. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0108036.
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Kulikova, D. B., E. V. Prazdnova, K. A. Demin, M. S. Mazanko, F. Y. Morgan-Blanche, and A. V. Gorovtsov. "MODELING CONDITIONS FOR CULTIVATION OF SOIL MICROORGANISMS." In STATE AND DEVELOPMENT PROSPECTS OF AGRIBUSINESS. ООО «ДГТУ-Принт» Адрес полиграфического предприятия: 344003, г. Ростов-на-Дону, пл. Гагарина,1., 2024. http://dx.doi.org/10.23947/interagro.2024.152-155.
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The share of microorganisms cultivated in laboratory conditions from the total diversity of prokaryotes is no more than 0.1%. At the same time, with the help of metagenomic and metatranscriptomic analysis methods, it is annually possible to identify new taxonomic groups of microorganisms that do not have cultivated representatives. One of the most important parameters affecting the cultivability of microorganisms is the composition of atmospheric gases in the environment. The study analyzed the cultivated part of the soil microbial community under conditions of high CO2 content, namely 5% of the composition of the gas mixture, in oligotrophic media.
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Kameneva, I., T. Melnichuk, S. Abdurashitov, E. Andronov, A. Yakubovskaya, M. Gritchin, and A. Prikhodko. "The taxonomic composition of the microbial community of the southern chernozem when introducing plant substrates and their destructors." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.109.
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The influence of green manure (phacelia), wheat straw, and cellulolytic association on the taxonomic structure of chernozems southern in the steppe zone of the Crimea was studied. Changes in the proportion among representatives of 11 phila, 14 bacteria, and 2 archaea were established.
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Turner, Christina A., and Craig Moyer. "TAXONOMIC AND FUNCTIONAL ANALYSIS OF MICROBIAL MAT COMMUNITIES OF MARIANA REGION HYDROTHERMAL VENTS." In GSA Annual Meeting in Seattle, Washington, USA - 2017. Geological Society of America, 2017. http://dx.doi.org/10.1130/abs/2017am-308566.
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Puhalsky, Ya V., S. I. Loskutov, E. M. Lapteva, Yu A. Vinogradova, V. A. Kovaleva, and E. M. Perminova. "The effect of organic fertilizers on the taxonomic composition of microbial communities in agro-soddy-podzolic soils of the middle taiga." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.201.
Full textReports on the topic "Microbial taxonomy"
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
Full textAbstract:
Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report
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Mizrahi, Itzhak, and Bryan A. White. Exploring the role of the rumen microbiota in determining the feed efficiency of dairy cows. United States Department of Agriculture, October 2011. http://dx.doi.org/10.32747/2011.7594403.bard.
Full textAbstract:
Expanding world hunger calls for increasing available food resources. Ruminants have the remarkable ability to convert human-indigestible plant biomass into human-digestible food products, due to a complex microbiome residing in the rumen compartment of their upper digestive tract. One way to tackle the problem of diminishing food resources is to increase the animals' energetic efficiency, i.e., the efficiency with which they convert energy from feed, thereby increasing food availability while lowering the environmental burden, as these animals would produce more and eat less. We hypothesize that the cow's feed efficiency is dependent on the taxonomic composition, coding capacity and activity of its reticulorumenmicrobiota. To test this hypothesis, three aims are defined: (1) Evaluation of the feed efficiency of 146 dairy cows and defining two groups representing the highest and lowest 25% using the Israeli group's unique facility; (2) Comparing these two groups for microbiota diversity, identity and coding capacity using next-generation sequencing and metagenomic approaches; (3) Comparing the reticulorumenmicrobiota metabolic activity parameters. We measured feed efficiency in 146 milking cows and analyzed the taxonomic composition, gene content, microbial activity and metabolomic composition of rumen microbiomes from the 78 most extreme animals. Lower richness of microbiome gene content and taxa was tightly linked to higher feed efficiency. Microbiome genes and species accurately predicted the animals' feed-efficiency phenotype. Specific enrichment of microbes and metabolic pathways in each of these microbiome groups resulted in increasing valuable metabolites and decreasing unusable ones such as methane in efficient animals. This ecological and mechanistic understanding of the rumen microbiome could lead to an increase in available food resources and environmentally friendly livestock agriculture.
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Weinberg, Zwi G., Adegbola Adesogan, Itzhak Mizrahi, Shlomo Sela, Kwnag Jeong, and Diwakar Vyas. effect of selected lactic acid bacteria on the microbial composition and on the survival of pathogens in the rumen in context with their probiotic effects on ruminants. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598162.bard.
Full textAbstract:
This research project was performed in context of the apparent probiotic effect of selected lactic acid bacteria (LAB) silage inoculants on the performance of ruminants (improved feed intake, faster live-weight gain, higher milk yields and improved feed efficiency). The overall objective was to find out how LAB affect ruminant performance. The project included several “chapters” as follows: 1. The effect of LAB silage inoculants on the survival of detrimental bacteria in rumen fluid, in vitro study (Weinberg et al., The Volcani Center). An in vitro model was developed to study the interaction between selected LAB and an E. coli strain tagged with green fluorescence protein (GFP) in buffered RF. Results indicated that both LAB inoculants and E. coli survived in the RF for several days; both LAB inoculants and LAB-treated silages did not affect survival of E. coli in rumen fluid in vitro. The effect of feeding baled wheat silages treated with or without three selected LAB silage inoculants on the performance of high-lactating cows (Weinberg et al., The Volcani Center). Treatments included control (no additive), Lacobacillusbuchneri40788 (LB), Lactobacillus plantarumMTD1 40027 (LP) and Pediococcuspentosaceus30168 (PP), each applied at 10⁶ cfu/g FM. The silages were included in the TMR of 32 high milking Holstein cows in a controlled feeding experiment. All baled silages were of good quality. The LB silage had the numerically highest acetic acid and were the most stable upon aerobic exposure. The cows fed the LB silages had the highest daily milk yields, percent milk fat and protein. The microbiome of baled wheat silages and changes during ensiling of wheat and corn (Sela et al., The Volcani Center). Bacterial community of the baled silages was dominated mainly of two genera in total, dominated by Lactobacillus and Clostridium_sensu_stricto_12 with 300 other genera at very low abundance. Fungal community was composed mainly of two genera in total, dominated by Candida and Monascuswith 20 other genera at very low abundance. In addition, changes in the microbiome during ensiling of wheat and corn with and without addition of L. plantarumMTD1 was studied in mini-silos. Overall 236 bacterial genera were identified in the fresh corn but after 3 months Lactobacillus outnumbered all other species by acquiring 95% of relative abundance. The wheat silage samples are still under analysis. The effect of applying LAB inoculants at ensiling on survival of E. coli O157:H7 in alfalfa and corn silages(Adesogan et al., University of Florida). E. coli (10⁵ cfu/g) was applied to fresh alfalfa and corn at ensiling with or without L. plantarumor L. buchneri. The pathogen was added again after about 3 moths at the beginning of an aerobic exposure period. The inoculants resulted in faster decrease in pH as compared with the control (no additives) or E. coli alone and therefore, the pathogen was eliminated faster from these silages. After aerobic exposure the pathogen was not detected in the LAB treated silages, whereas it was still present in the E. coli alone samples. 5. The effect of feeding corn silage treated with or without L. buchnerion shedding of E. coli O157:H7 by dairy cows (Adesogan et al., UFL). BARD Report - Project 4704 Page 2 of 12 Five hundred cows from the dairy herd of the University of Florida were screened for E. coli shedding, out of which 14 low and 13 high shedders were selected. These cows were fed a total mixed ration (TMR) which was inoculated with E. coli O157:H7 for 21 days. The TMR included corn silage treated with or without L. buchneri. The inoculated silages were more stable upon aerobic exposure than the control silages; the silage inoculant had no significant effect on any milk or cow blood parameters. However, the silage inoculant tended to reduce shedding of E. coli regardless of high or low shedders (p = 0.06). 6. The effect of feeding baled wheat silages treated with or without three selected LAB silage inoculants on the rumen microbiome (Mizrahi et al., BGU). Rumen fluid was sampled throughout the feeding experiment in which inoculated wheat silages were included in the rations. Microbial DNA was subsequently purified from each sample and the 16S rRNA was sequenced, thus obtaining an overview of the microbiome and its dynamic changes for each experimental treatment. We observed an increase in OTU richness in the group which received the baled silage inoculated with Lactobacillus Plantarum(LP). In contrast the group fed Lactobacillus buchneri(LB) inoculated silage resulted in a significant decrease in richness. Lower OTU richness was recently associated in lactating cows with higher performance (Ben Shabatet al., 2016). No significant clustering could be observed between the different inoculation treatments and the control in non metric multi-dimentional scaling, suggesting that the effect of the treatments is not the result of an overall modulation of the microbiome composition but possibly the result of more discrete interactions. Significant phylum level changes in composition also indicates that no broad changes in taxa identity and composition occurred under any treatment A more discrete modulation could be observed in the fold change of several taxonomic groups (genus level analysis), unique to each treatment, before and after the treatment. Of particular interest is the LB treated group, in which several taxa significantly decreased in abundance. BARD Report - Project 4704 Page 3 of 12