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Journal articles on the topic 'Microbial taxonomy'

Author: Grafiati

Published: 8 November 2024

Last updated: 31 July 2025

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1

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 (2021): 394–404. http://dx.doi.org/10.1016/j.tim.2020.12.010.

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3

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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4

Goldberg, Martin. "Microbial classification, taxonomy, & identification." Biomedical & Life Sciences Collection 2025, no. 2 (2025): e1006610. https://doi.org/10.69645/kjbc5139.

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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 (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 th

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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 (2010): 430–38. http://dx.doi.org/10.1016/j.resmic.2010.05.007.

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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 (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 conf

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Tamames, Javier, and Ramon Rosselló-Móra. "On the fitness of microbial taxonomy." Trends in Microbiology 20, no. 11 (2012): 514–16. http://dx.doi.org/10.1016/j.tim.2012.08.012.

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9

Green, J. L., B. J. M. Bohannan, and R. J. Whitaker. "Microbial Biogeography: From Taxonomy to Traits." Science 320, no. 5879 (2008): 1039–43. http://dx.doi.org/10.1126/science.1153475.

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Bik, Holly. "Complexity matters: Evaluating the impact of bioinformatics parameters on eukaryotic MOTU delimitation and taxonomy assignment." ARPHA Conference Abstracts 4 (March 4, 2021): e65374. https://doi.org/10.3897/aca.4.e65374.

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Microbial metazoans (e.g. nematodes, copepods, tardigrades and other 'minor' animal phyla < 1mm in size) are ubiquitous and abundant across most ecosystems on earth. In marine sediment habitats, microbial metazoa exhibit high biodiversity but suffer from poor taxonomy and an ongoing lack of reference DNA sequences in public databases. Environmental DNA metabarcoding thus represents an increasingly critical tool for rapidly assessing the global biodiversity and phylogeographic patterns of such neglected metazoan groups. However, there are significant bioinformatics hurdles facing the study o

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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 (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

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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 (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 sequen

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Hugenholtz, Philip, Adam Skarshewski, and Donovan H. Parks. "Genome-Based Microbial Taxonomy Coming of Age." Cold Spring Harbor Perspectives in Biology 8, no. 6 (2016): a018085. http://dx.doi.org/10.1101/cshperspect.a018085.

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SUZUKI, KEN-ICIRO. "New trend in microbial taxonomy. 2. Chemotaxonomy." Kagaku To Seibutsu 26, no. 12 (1988): 858–64. http://dx.doi.org/10.1271/kagakutoseibutsu1962.26.858.

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15

Kersters, Karel. "Macromolecular fingerprints and data bases in microbial taxonomy." Fresenius' Journal of Analytical Chemistry 343, no. 1 (1992): 48–49. http://dx.doi.org/10.1007/bf00331994.

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KOMAGATA, KAZUO. "New direction of microbial taxonomy. 1 Its trends." Kagaku To Seibutsu 26, no. 10 (1988): 674–81. http://dx.doi.org/10.1271/kagakutoseibutsu1962.26.674.

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Ruchi Yadav, Aditi Kumari. "Exploring Soil Microbiomes Through Metagenomic Analysis: Taxonomy and Function." International Scientific Journal of Engineering and Management 04, no. 05 (2025): 1–9. https://doi.org/10.55041/isjem03617.

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Abstract Soil metagenomics is a rapidly advancing approach that enables the exploration of soil microbial communities without the need for cultivation, providing valuable insights into their diversity, metabolic functions, and ecological roles. In this study, we utilized metagenomic analysis of soil samples retrieved from the MGnify database (project ID: PRJDB5367), using 16S rRNA gene sequencing data. A comprehensive analysis was performed on the Galaxy Server platform. The results identified several key bacterial taxa, including Gammaproteobacteria, Streptosporangium longisporum, and Sporomu

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Chuvochina, Maria, Christian Rinke, Aaron Mussig, Pierre-Alain Chaumeil, Donovan Parks, and Philip Hugenholtz. "Genome Taxonomy Database and SeqCode: Microbial taxonomy and nomenclature in the age of big sequence data." Biodiversity Information Science and Standards 7 (August 16, 2023): e111135. https://doi.org/10.3897/biss.7.111135.

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Microbial taxonomy and nomenclature have been challenged by methodological advances in high-throughput sequencing and high-performance computing. While taxonomy appears to adapt rapidly and has benefited enormously from the availability of whole-genome sequences, nomenclature still struggles to embrace these changes. Here, we present two independent initiatives that have resulted from the transitions of taxonomic practices in microbiology from a phenotypic and single gene-driven framework to a genome-based driven framework.The first initiative, the Genome Taxonomy Database (GTDB), was develope

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Gladka, G. V., N. V. Borzova, O. V. Gudzenko, V. M. Hovorukha, О. А. Havryliuk, and О. B. Tashyrev. "Polyphase Taxonomy of Antarctic Bacteria." Mikrobiolohichnyi Zhurnal 83, no. 3 (2021): 3–13. http://dx.doi.org/10.15407/microbiolj83.03.003.

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The phylogenetic structure of bacteria is not always consistent with the traditional classification scheme based on the phenotypic properties of bacteria. That is one of the problems of modern bacterial taxonomy. In addition, traditional methods to identify bacteria using phenotypic properties have a number of disadvantages. In recent decades, significant progress was achieved in the investigation of microbial world using molecular methods for fast identification. The aim of the study was to clarify the species status of four strains of bacteria isolated from black lichens of the cliffs of Gal

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20

Xing, Haixia, Hongwei Liu, and Jie Pan. "High-Throughput Sequencing of Oral Microbiota in Candida Carriage Sjögren’s Syndrome Patients: A Pilot Cross-Sectional Study." Journal of Clinical Medicine 12, no. 4 (2023): 1559. http://dx.doi.org/10.3390/jcm12041559.

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Background: This study sought to characterize the saliva microbiota of Candida carriage Sjögren’s syndrome (SS) patients compared to oral candidiasis and healthy patients by high-throughput sequencing. Methods: Fifteen patients were included, with five Candida carriage SS patients (decayed, missing, and filled teeth (DMFT) score 22), five oral candidiasis patients (DMFT score 17), and five caries active healthy patients (DMFT score 14). Bacterial 16S rRNA was extracted from rinsed whole saliva. PCR amplification generated DNA amplicons of the V3–V4 hypervariable region, which were sequenced on

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Woese, C. R. "Default taxonomy: Ernst Mayr's view of the microbial world." Proceedings of the National Academy of Sciences 95, no. 19 (1998): 11043–46. http://dx.doi.org/10.1073/pnas.95.19.11043.

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Fredrickson, Herbert. "Applications of methods of chemical analysis in microbial taxonomy." Fresenius' Journal of Analytical Chemistry 343, no. 1 (1992): 47–48. http://dx.doi.org/10.1007/bf00331992.

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Larsen, Thomas O., Jørn Smedsgaard, Kristian F. Nielsen, Michael E. Hansen, and Jens C. Frisvad. "Phenotypic taxonomy and metabolite profiling in microbial drug discovery." Natural Product Reports 22, no. 6 (2005): 672. http://dx.doi.org/10.1039/b404943h.

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Chen, Huaihai, Kayan Ma, Yu Huang, et al. "Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics." SOIL 8, no. 1 (2022): 297–308. http://dx.doi.org/10.5194/soil-8-297-2022.

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Abstract. Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes than with “narrow” functions in which specific microorganisms specialize. Thus, a comprehensive study to

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25

Montero, Angel, M. Elias Dueker, and Gregory D. O’Mullan. "Culturable bioaerosols along an urban waterfront are primarily associated with coarse particles." PeerJ 4 (December 22, 2016): e2827. http://dx.doi.org/10.7717/peerj.2827.

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The source, characteristics and transport of viable microbial aerosols in urban centers are topics of significant environmental and public health concern. Recent studies have identified adjacent waterways, and especially polluted waterways, as an important source of microbial aerosols to urban air. The size of these aerosols influences how far they travel, their resistance to environmental stress, and their inhalation potential. In this study, we utilize a cascade impactor and aerosol particle monitor to characterize the size distribution of particles and culturable bacterial and fungal aeroso

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Nadkarni, Mangala, Roy Byun, and Kim-Ly Chhour. "Molecular taxonomy of polymicrobial diseases ? finding novel bacteria not previously considered to be associated with oral diseases." Microbiology Australia 26, no. 3 (2005): 117. http://dx.doi.org/10.1071/ma05117.

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Recombinant DNA technology and molecular biology have brought a revolution to the limitations imposed by traditional taxonomic methods of bacterial identification based solely on cultivation. Following on from the novel research of Carl Woese, molecular taxonomy is generally based on variations in the sequence of the 16S rRNA gene and has brought a new perspective to our understanding of the diversity of uncultured bacteria in a multitude of microbial habitats. Analysis of the polymicrobial oral diseases is no exception.

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Chanson, Anaïs, Corrie S. Moreau, and Christophe Duplais. "Impact of Nesting Mode, Diet, and Taxonomy in Structuring the Associated Microbial Communities of Amazonian Ants." Diversity 15, no. 2 (2023): 126. http://dx.doi.org/10.3390/d15020126.

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Studies of ant biodiversity are important to understand their group better, as well as to extend our knowledge on the evolution of their associated organisms. Host-associated microbial communities, and particularly bacterial communities, are shaped by different host factors such as habitat, diet, and phylogeny. Here, we studied the structures of bacterial and microbial eukaryote communities associated with Amazonian ants collected from two habitats: the rainforest and the city. We collected 38 ant species covering a large taxonomic range, and we used 16S rRNA and 18S rRNA amplicon sequencing t

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Ranasinghe, Purnika Damindi, Hiroyasu Satoh, Mamoru Oshiki, et al. "Revealing microbial community structures in large- and small-scale activated sludge systems by barcoded pyrosequencing of 16S rRNA gene." Water Science and Technology 66, no. 10 (2012): 2155–61. http://dx.doi.org/10.2166/wst.2012.428.

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The diversity of bacterial groups in activated sludge from large- and small-scale wastewater treatment plants was explored by barcoded pyrosequencing of 16S rRNA gene. Activated sludge samples (three small and 17 large scale) were collected from 12 wastewater treatment plants to clarify precise taxonomy and relative abundances. DNA was extracted, and amplified by 4 base barcoded 27f/519r primer set. The 454 Titanium (Roche) pyrosequences were obtained and analyses performed by Quantitative Insight Into Microbial Ecology (QIIME) with around 100,000 reads. Sequence statistics were computed, whil

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Ramírez-Flandes, Salvador, Bernardo González, and Osvaldo Ulloa. "Redox traits characterize the organization of global microbial communities." Proceedings of the National Academy of Sciences 116, no. 9 (2019): 3630–35. http://dx.doi.org/10.1073/pnas.1817554116.

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The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a gen

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de la Cuesta-Zuluaga, Jacobo, Ruth E. Ley, and Nicholas D. Youngblut. "Struo: a pipeline for building custom databases for common metagenome profilers." Bioinformatics 36, no. 7 (2019): 2314–15. http://dx.doi.org/10.1093/bioinformatics/btz899.

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Abstract Summary Taxonomic and functional information from microbial communities can be efficiently obtained by metagenome profiling, which requires databases of genes and genomes to which sequence reads are mapped. However, the databases that accompany metagenome profilers are not updated at a pace that matches the increase in available microbial genomes, and unifying database content across metagenome profiling tools can be cumbersome. To address this, we developed Struo, a modular pipeline that automatizes the acquisition of genomes from public repositories and the construction of custom da

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Miaow, Katie, Donnabella Lacap-Bugler, and Hannah L. Buckley. "Identifying optimal bioinformatics protocols for aerosol microbial community data." PeerJ 9 (September 30, 2021): e12065. http://dx.doi.org/10.7717/peerj.12065.

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Microbes are fundamental to Earth’s ecosystems, thus understanding ecosystem connectivity through microbial dispersal is key to predicting future ecosystem changes in a warming world. However, aerial microbial dispersal remains poorly understood. Few studies have been performed on bioaerosols (microorganisms and biological fragments suspended in the atmosphere), despite them harboring pathogens and allergens. Most environmental microbes grow poorly in culture, therefore molecular approaches are required to characterize aerial diversity. Bioinformatic tools are needed for processing the next ge

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Van den Meersche, Karel, Karline Soetaert, and Jack J. Middelburg. "A Bayesian compositional estimator for microbial taxonomy based on biomarkers." Limnology and Oceanography: Methods 6, no. 5 (2008): 190–99. http://dx.doi.org/10.4319/lom.2008.6.190.

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Meier-Kolthoff, Jan P., Markus Göker, Cathrin Spröer, and Hans-Peter Klenk. "When should a DDH experiment be mandatory in microbial taxonomy?" Archives of Microbiology 195, no. 6 (2013): 413–18. http://dx.doi.org/10.1007/s00203-013-0888-4.

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Thompson, Cristiane C., Gilda R. Amaral, Mariana Campeão, et al. "Microbial taxonomy in the post-genomic era: Rebuilding from scratch?" Archives of Microbiology 197, no. 3 (2014): 359–70. http://dx.doi.org/10.1007/s00203-014-1071-2.

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35

Bell, Terrence H., Franck O. P. Stefani, Katrina Abram, et al. "A Diverse Soil Microbiome Degrades More Crude Oil than Specialized Bacterial Assemblages Obtained in Culture." Applied and Environmental Microbiology 82, no. 18 (2016): 5530–41. http://dx.doi.org/10.1128/aem.01327-16.

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ABSTRACTSoil microbiome modification may alter system function, which may enhance processes like bioremediation. In this study, we filled microcosms with gamma-irradiated soil that was reinoculated with the initial soil or cultivated bacterial subsets obtained on regular media (REG-M) or media containing crude oil (CO-M). We allowed 8 weeks for microbiome stabilization, added crude oil and monoammonium phosphate, incubated the microcosms for another 6 weeks, and then measured the biodegradation of crude oil components, bacterial taxonomy, and functional gene composition. We hypothesized that t

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Bouras, Noureddine, Imen Nouioui, Guendouz Dif, Fawzia Chaabane Chaouch, and Sherif S. Ebada. "Whole genome-based reclassification of several species of the genus Nonomuraea." PLOS One 20, no. 7 (2025): e0327003. https://doi.org/10.1371/journal.pone.0327003.

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Earlier classification methods lacked the resolution necessary to delineate species comparing to current standards, particularly since a significant number of bacterial taxa were described before the integration of whole-genome sequencing into microbial taxonomy. With the advent of genome-based taxonomic approaches and integrated genomic metrics, including sequence similarity and phylogenomic frameworks, it has become essential to reevaluate the taxonomic status of older taxa defined before the era of genome-based microbial taxonomy. Applying these modern genomic criteria enables a more accura

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Zheng, Xiang, Qidi Zhu, Zhijun Zhou, et al. "Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits." PLOS ONE 16, no. 4 (2021): e0250675. http://dx.doi.org/10.1371/journal.pone.0250675.

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Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed

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Ramesh, Chatragadda, and Laurent Dufossé. "Blue Microbiology—Aquatic Microbial Resources for Sustainable Life on Earth." Microorganisms 11, no. 3 (2023): 808. http://dx.doi.org/10.3390/microorganisms11030808.

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Bolduc, Benjamin, Ho Bin Jang, Guilhem Doulcier, Zhi-Qiang You, Simon Roux, and Matthew B. Sullivan. "vConTACT: an iVirus tool to classify double-stranded DNA viruses that infectArchaeaandBacteria." PeerJ 5 (May 3, 2017): e3243. http://dx.doi.org/10.7717/peerj.3243.

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Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked aga

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van Belkum, Alex, Marc Struelens, Arjan de Visser, Henri Verbrugh, and Michel Tibayrenc. "Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology." Clinical Microbiology Reviews 14, no. 3 (2001): 547–60. http://dx.doi.org/10.1128/cmr.14.3.547-560.2001.

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SUMMARY Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of ge

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Anderson, O. Roger. "Microbial Respiration of Organic Carbon in Freshwater Microcosms: The Potential for Improved Estimation of Microbial CO Emission from Organically Enriched Freshwater Ecosystems." Acta Protozoologica 55, no. 3 (2016): 189–96. https://doi.org/10.4467/16890027AP.16.018.5750.

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Anderson, O. Roger (2016): Microbial Respiration of Organic Carbon in Freshwater Microcosms: The Potential for Improved Estimation of Microbial CO Emission from Organically Enriched Freshwater Ecosystems. Acta Protozoologica 55 (3): 189-196, DOI: 10.4467/16890027AP.16.018.5750, URL: https://www.mendeley.com/catalogue/f098019e-6b5e-3a10-80ea-d0f6580b0431/

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Zhou, Jiayin, Wei Qin, Xinda Lu, et al. "The diversity and ecological significance of microbial traits potentially involved in B₁₂ biosynthesis in the global ocean." mLife 2, no. 4 (2023): 416–27. http://dx.doi.org/10.1002/mlf2.12095.

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AbstractCobalamin (B12), an essential nutrient and growth cofactor for many living organisms on Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related to B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make‐up of complex functional assemblages. By anchoring microbial traits potentially involved in B12 biosynthesis, we depict the biogeographic patterns of B12 biosynthesis genes and the taxa harboring them in the global ocean, despite the limitat

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Flores, Roberto, Jianxin Shi, Mitchell H. Gail, Pawel Gajer, Jacques Ravel, and James J. Goedert. "Association of Fecal Microbial Diversity and Taxonomy with Selected Enzymatic Functions." PLoS ONE 7, no. 6 (2012): e39745. http://dx.doi.org/10.1371/journal.pone.0039745.

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Huse, Susan M., Les Dethlefsen, Julie A. Huber, David Mark Welch, David A. Relman, and Mitchell L. Sogin. "Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing." PLoS Genetics 4, no. 11 (2008): e1000255. http://dx.doi.org/10.1371/journal.pgen.1000255.

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Fenwick, Alexander J., and Karen C. Carroll. "Practical problems when incorporating rapidly changing microbial taxonomy into clinical practice." Clinical Chemistry and Laboratory Medicine (CCLM) 57, no. 9 (2019): e238-e240. http://dx.doi.org/10.1515/cclm-2018-1068.

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Jaba, Asma, Fadi Dagher, Amir Mehdi Hamidi Oskouei, Claude Guertin, and Philippe Constant. "Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds." Canadian Journal of Microbiology 65, no. 9 (2019): 668–80. http://dx.doi.org/10.1139/cjm-2019-0052.

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Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess d

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Remenyik, Judit, László Csige, Péter Dávid, et al. "Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region." PLOS ONE 19, no. 4 (2024): e0300563. http://dx.doi.org/10.1371/journal.pone.0300563.

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A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four hist

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Shabangu, Khaya Pearlman, Manimagalay Chetty, and Babatunde Femi Bakare. "Metagenomic Insights into Pollutants in Biorefinery and Dairy Wastewater: rDNA Dominance and Electricity Generation in Double Chamber Microbial Fuel Cells." Bioengineering 12, no. 1 (2025): 88. https://doi.org/10.3390/bioengineering12010088.

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This study evaluates the potential of biorefinery and dairy wastewater as substrates for electricity generation in double chamber Microbial Fuel Cells (DCMFC), focusing on their microbial taxonomy and electrochemical viability. Taxonomic analysis using 16S/18S rDNA-targeted DGGE and high-throughput sequencing identified Proteobacteria as dominant in biorefinery biomass, followed by Firmicutes and Bacteriodota. In dairy biomass, Lactobacillus (77.36%) and Clostridium (15.70%) were most prevalent. Biorefinery wastewater exhibited the highest bioelectrochemical viability due to its superior elect

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Royalty, Taylor M., and Andrew D. Steen. "Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life." mSphere 4, no. 4 (2019). http://dx.doi.org/10.1128/msphere.00446-19.

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ABSTRACT Widely used microbial taxonomies, such as the NCBI taxonomy, are based on a combination of sequence homology among conserved genes and historically accepted taxonomies, which were developed based on observable traits such as morphology and physiology. A recently proposed alternative taxonomy database, the Genome Taxonomy Database (GTDB), incorporates only sequence homology of conserved genes and attempts to partition taxonomic ranks such that each rank implies the same amount of evolutionary distance, regardless of its position on the phylogenetic tree. This provides the first opportu

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Chen, Huaihai, Kayan Ma, Yu Huang, Yuchun Yang, Zilong Ma, and Chengjin Chu. "Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes." Frontiers in Microbiology 12 (November 1, 2021). http://dx.doi.org/10.3389/fmicb.2021.719725.

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A tight association between microbial function and taxonomy is the basis of functional prediction based on taxonomy, but such associations have been controversial in water biomes largely due to the probable prevalence of functional redundancy. However, previous studies on this topic used a relatively coarse resolution of ecosystem functioning, potentially inflating the estimated functional redundancy. Thus, a comprehensive evaluation of the association between high-resolution functional traits and taxonomic diversity obtained from fresh and saline water metagenomic data is urgently needed. Her

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