Microbial Bioactives
Microbial Bioactives | Online ISSN 2209-2161
295
Citations
205.5k
Views
181
Articles
Volume 6 Number 1 2023
REVIEWS (Open Access)
Advancements in Microbiome Analysis of Pathogenic Microorganisms: From Culture-Dependent Methods to Integrated Meta-Omics Approaches
Jegathambigai Rameshwar Naidu 1, Mahfoudh A.M. Abdulghani 2*
Microbial Bioactives 6 (1) 1-8 https://doi.org/10.25163/microbbioacts.6110673
Submitted: 17 March 2023 Revised: 14 May 2023 Accepted: 21 May 2023 Published: 23 May 2023
Abstract
The study of microbiomes and their associated pathogens has evolved dramatically, transitioning from culture-dependent approaches to integrated high-throughput sequencing (HTS) and meta-omics analyses. Historically, only a small fraction of microbial diversity could be assessed due to the limitations of traditional cultivation methods, leaving the majority of microbial life unexplored. Modern technologies, including second- and third-generation sequencing platforms, have revolutionized this field by enabling comprehensive characterization of microbial communities in both terrestrial and marine ecosystems. Metabarcoding and shotgun metagenomics now allow for detailed taxonomic profiling, functional gene prediction, and identification of emerging pathogens at the species or strain level. High-fidelity in situ sampling tools, such as pressure-retaining samplers and microbial filtration devices, preserve native microbial physiology, providing a more accurate representation of environmental microbial activity. Complementary techniques including quantitative PCR, droplet digital PCR, and CARD-FISH enhance pathogen detection and quantification, while integrated meta-omics approaches—metatranscriptomics, proteomics, and metabolomics—allow researchers to distinguish active microbial populations from dormant or extracellular DNA, elucidating functional interactions within the microbiome. Bioinformatic pipelines, including QIIME2, DADA2, and CoMA, facilitate the analysis of complex datasets, providing high-resolution insights into microbial dynamics and host-pathogen interactions. This systematic review and meta-analysis highlight the advances, challenges, and opportunities in microbiome research, underscoring the critical role of technological innovations in monitoring microbial pathogens across diverse environmental contexts.
Keywords: microbiome, high-throughput sequencing, meta-omics, metabarcoding, shotgun metagenomics, microbial pathogens, in situ sampling, qPCR, droplet digital PCR
References
Abad, Z. G., Ivors, K. L., Gallup, C. A., Abad, J. A., Shew, H. D., & Widmer, T. L. (2019). Metabarcoding identification of Phytophthora species via MinION high-throughput sequencing. IUFRO Proceedings. https://doi.org/10.3390/f12020229
Aragona, M., Cacciola, S. O., Pane, A., & Magnano di San Lio, G. (2022). New-generation sequencing technology in the diagnosis of fungal plant pathogens. Journal of Fungi, 8(7), 737. https://doi.org/10.3390/jof8070737
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583. https://doi.org/10.1038/nmeth.3869
Chang, J. J., Ip, Y. C. A., Ng, C. S. L., & Huang, D. (2020). Takeaways from mobile DNA barcoding with BentoLab and MinION. Genes, 11(10), 1121. https://doi.org/10.3390/genes11101121
Edgcomb, V. P., Orsi, W., Bunge, J., Jeon, S., Christen, R., Leslin, C., Holder, M., Taylor, G. T., Suarez, P., & Varela, R. (2016). Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep-sea microbial communities. Deep-Sea Research Part II: Topical Studies in Oceanography, 129, 213–222. https://doi.org/10.1016/j.dsr2.2014.10.020
Figueras, A., Moreira, R., Sendra, M., & Novoa, B. (2019). Genomics and immunity of Mytilus galloprovincialis. Fish & Shellfish Immunology, 90, 440–445. https://doi.org/10.1016/j.fsi.2019.04.022
He, S., Wang, Y., Zhang, Y., Huang, X., Zhang, J., & Xiao, X. (2023). A novel submersible-mounted sediment pressure-retaining sampler for deep-sea microbiological research. Frontiers in Marine Science, 10, 1154269. https://doi.org/10.3389/fmars.2023.1154269
Huang, Z., Zhang, X., Li, J., Chen, Y., & Zhang, Y. (2023). Technological advancements in field investigations of marine microorganisms. Journal of Marine Science and Engineering, 11, 1981. https://doi.org/10.3390/jmse11101981
Hupfauf, S., Winkler, M., Wagner, A. O., Podmirseg, S. M., & Insam, H. (2020). CoMA—An intuitive pipeline for amplicon sequencing data analysis. PLOS ONE, 15, e0243241. https://doi.org/10.1371/journal.pone.0243241
Kim, T. G., Jeong, S. Y., & Cho, K. S. (2014). Comparison of droplet digital PCR and quantitative PCR for quantification of bacteria in soil. Applied Microbiology and Biotechnology, 98, 6105–6113. https://doi.org/10.1007/s00253-014-5744-1
Knight, R., Callewaert, C., Marotz, C., Hyde, E. R., Debelius, J. W., McDonald, D., & Sogin, M. L. (2018). Best practices for analysing microbiomes. Nature Reviews Genetics, 16, 410–422. https://doi.org/10.1038/nrg.2017.58
Landa, B. B., Montes-Borrego, M., Muñoz-Ledesma, F. J., Jiménez-Díaz, R. M., & Castillo, P. (2021). Diversity of Phytophthora species in British soils assessed using high-throughput sequencing. Forests, 12(2), 229. https://doi.org/10.3390/f12020229
Li, L. L., Wang, Y., Cai, L., Li, Y., Chen, X., & He, L. (2020). Impacts of microplastics exposure on gut microbiota of the mussel Mytilus galloprovincialis. Science of the Total Environment, 745, 141018. https://doi.org/10.1016/j.scitotenv.2020.141018
Liu, S., Vijayendran, D., & Bonning, B. C. (2011). Next generation sequencing technologies for insect virus discovery and analysis. Viruses, 3, 1849–1869. https://doi.org/10.3390/v3101849
Maestri, S., Cosentino, E., Paterno, M., Freitag, H., Garces, J. M., Marcolungo, L., Alfano, M., Njunjic, I., Schilthuizen, M., Slik, J. W. F., Menegon, M., & Rossato, M. (2019). A rapid and accurate MinION-based DNA barcoding pipeline for species biodiversity assessment. Genes, 10, 468. https://doi.org/10.3390/genes10060468
McLennan, K., Hinder, S. L., Brown, M. R., & Davidson, K. (2021). Assessing molecular barcoding and qPCR approaches for detecting Prorocentrum minimum. Microorganisms, 9(3), 510. https://doi.org/10.3390/microorganisms9030510
Nilsson, R. H., Anslan, S., Bahram, M., Wurzbacher, C., Baldrian, P., & Tedersoo, L. (2019). Mycobiome diversity: High-throughput sequencing and identification of fungi. Nature Reviews Microbiology, 17, 95–109. https://doi.org/10.1038/s41579-018-0116-y
Page, M. J., McKenzie, J. E., Bossuyt, P. M., Boutron, I., Hoffmann, T. C., Mulrow, C. D., Shamseer, L., Tetzlaff, J. M., Akl, E. A., Brennan, S. E., Chou, R., Glanville, J., Grimshaw, J. M., Hróbjartsson, A., Lalu, M. M., Li, T., Loder, E. W., Mayo-Wilson, E., McDonald, S., … Moher, D. (2021). The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. BMJ, 372, n71. https://doi.org/10.1136/bmj.n71
Page, T. M., & Lawley, J. W. (2022). A review of transcriptomic approaches in marine ecology. Frontiers in Marine Science, 9, 757921. https://doi.org/10.3389/fmars.2022.757921
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017). Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35, 833–844. https://doi.org/10.1038/nbt.3935
Sam, Q. H., Chang, M. W., & Chai, L. Y. A. (2017). The fungal mycobiome and its interaction with gut bacteria. International Journal of Molecular Sciences, 18(2), 330. https://doi.org/10.3390/ijms18020330
Schoenle, A., Hohlfeld, M., Hermanns, K., & Arndt, H. (2016). Estimates of heterotrophic flagellates from the deep-sea floor. Journal of Marine Science and Engineering, 4, 22. https://doi.org/10.3390/jmse4010022
Schoinas, K., Giannoulis, A., Louvrou, I., & Kormas, K. A. (2023). Microbiome profile of the Mediterranean mussel Mytilus galloprovincialis. Diversity, 15(3), 463. https://doi.org/10.3390/d15030463
Taylor, J., Stockdale, A., & Hill, P. G. (2015). In situ microbial filtration and incubation devices for aquatic ecosystems. Environmental Microbiology Reports, 7, 520–529. https://doi.org/10.1111/1758-2229.12312
Vargas-Gastélum, L., & Riquelme, M. (2020). The mycobiota of the deep sea. Life, 10(11), 292. https://doi.org/10.3390/life10110292
Velasco-González, I., González, M. C., & Santos-Guerra, A. (2023). Pathogenic eukaryotic microorganisms inhabiting mountain rocks. Diversity, 15(5), 594. https://doi.org/10.3390/d15050594
Wydro, U. (2022). Soil microbiome studies based on DNA extraction methods: A review. Water, 14, 3999. https://doi.org/10.3390/w14243999
Recommended articles
Microbial Frontiers in Extreme Environments: Rethinking Bioactive Potential Across Marine and Pristine Ecosystems
Marine Microbial Metabolites as Bioactive Reservoirs: A Systematic Synthesis of Biosynthetic Diversity and Functional Potential
Illuminating Biological Dark Matter: Integrating Metagenomics, Synthetic Biology, and AI to Unlock Microbial and Genomic Potential for Therapeutics and Biotechnology
Article metrics
View details
0
Downloads
0
Citations
6
Views
0
Save
Save
0
Citation
Citation
6
View
View
0
Share
Share