Abstract
Microbes, including bacteria, archaea, fungi, and viruses, are fundamental to our ecosystems, health, and industries. Microbial data analysis has become indispensable in understanding their roles and interactions. In this era of big data, advanced techniques, such as high-throughput sequencing, metagenomics, and bioinformatics, have accelerated microbial research. This chapter explores the significance of intelligent techniques, particularly machine learning and artificial intelligence, in revolutionizing microbial data analysis. The aim of this chapter is to showcase the pivotal role of intelligent techniques in microbial data analysis across diverse domains, from ecology and public health to biotechnology. We delve into case studies that highlight the practical applications of these techniques and the transformative impact they have had on microbial research. Several case studies are presented, illustrating the applications of intelligent techniques in microbial research. These include predicting disease risk through gut microbiome analysis, antibiotic resistance prediction, environmental microbiology for ecosystem management, bioprocess optimization in biotechnology, and AI-powered antibiotic susceptibility testing. Each case study demonstrates how intelligent techniques have enhanced data analysis, prediction, and decision-making in their respective domains. Microbial data analysis, driven by intelligent techniques, has ushered in a new era of understanding and harnessing the power of microorganisms. The future of microbial data analysis holds immense promise, with emerging trends including the integration of omics data, explainable AI, personalized microbiome analysis, and the development of ethical and regulatory frameworks. Collaborative research and data sharing are expected to further advance our understanding of the microbial world, offering solutions to some of the most critical challenges of our time.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Arif U, Bhatti KH, Ajaib M, Wagay NA, Majeed M, Zeb J, Hameed A, Kiani J (2021) Ethnobotanical indigenous knowledge of Tehsil Charhoi, District Kotli, Azad Jammu and Kashmir, Pakistan. Ethnobot Res Appl 22:1–24. https://doi.org/10.32859/ERA.22.50.1-24
Bashir SM, Altaf M, Hussain T, Umair M, Majeed M, Mangrio WM, Khan AM, Gulshan AB, Hamed MH, Ashraf S, Amjad MS, Bussmann RW, Abbasi AM, Casini R, Alataway A, Dewidar AZ, Al-Yafrsi M, Amin MH, Elansary HO (2023) Vernacular taxonomy, cultural and ethnopharmacological applications of avian and mammalian species in the vicinity of Ayubia National Park, Himalayan Region. Biology 12:4
Bates DW, Saria S, Ohno-Machado L, Shah A, Escobar G (2014) Big data in health care: using analytics to identify and manage high-risk and high-cost patients. Health Aff 33(7):1123–1131. https://doi.org/10.1377/hlthaff.2014.0041
Belkaid Y, Hand TW (2014) Role of the microbiota in immunity and inflammation. Cell 157(1):121–141
Brinegar K, DeDeo S, Lazer D (2021) Ethnicity and representation in academic machine learning discourse. arXiv:2104.05560
Bzdok D, Ioannidis JP (2019) Exploration, inference, and prediction in neuroscience and biomedicine. Trends Neurosci 42(4):251–262. https://doi.org/10.1016/j.tins.2019.02.003
Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Raj A (2020) Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genes Dev 34(7–8):440–451
Chen Y, Wang Q, Jiang H et al (2022) Machine learning models for enhanced bioethanol production through fermentation process optimization. Bioenergy Res:1–12
Esteva A, Robicquet A, Ramsundar B, Kuleshov V, DePristo M, Chou K, Dean J (2019) A guide to deep learning in healthcare. Nat Med 25(1):24–29
Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive Earth’s biogeochemical cycles. Science 320(5879):1034–1039. https://doi.org/10.1126/science.1153213
Forslund K, Hildebrand F, Nielsen T et al (2015) Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528(7581):262–266
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C (2018) Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol 16(11):591–606
Guttenberg N, Warfield K, Pickett BE, Ledogar RJ (2020) Brain size and network properties of human population genetic networks. Nat Commun 11(1):1–12. https://doi.org/10.1038/s41467-020-19135-w
Haberbeck LU, Wang X, Michiels C, Devlieghere F, Uyttendaele M, Geeraerd AH (2017) Cross-protection between controlled acid-adaptation and thermal inactivation for 48 Escherichia coli strains. Int J Food Microbiol 241:206–214
Haeuser E, Dawson N (2020) Microbiome data should be regulated as personal data. Nat Med 26(12):1806–1808
Haq SM, Yaqoob U, Majeed M, Amjad MS, Hassan M, Ahmad R, Morales-de la Nuez A (2022) Quantitative ethnoveterinary study on plant resource utilization by indigenous communities in high-altitude regions. Front Vet Sci 9:94404
Hassan M, Haq SM, Ahmad R, Majeed M, Sahito HA, Shirani M, Mubeen I, Aziz MA, Pieroni A, Bussmann RW, Alataway A, Dewidar AZ, Al-Yafrsi M, Elansary HO, Yessoufou K (2022a) Traditional use of wild and domestic fauna among different ethnic groups in the Western Himalayas? Cross cultural analysis. Animals 12:17
Hassan M, Haq SM, Majeed M, Umair M, Sahito HA, Shirani M, Waheed M, Aziz R, Ahmad R, Bussmann RW, Alataway A, Dewidar AZ, El-Abedin TKZ, Al-Yafrsi M, Elansary HO, Yessoufou K (2022b) Traditional food and medicine: ethno-traditional usage of fish fauna across the valley of Kashmir: a Western Himalayan region. Diversity 14:6
Holzinger A, Langs G, Denk H, Zatloukal K, Müller H (2017) Causability and explainability of artificial intelligence in medicine. Wiley Interdiscip Rev Data Mining Knowl Discov 7(6):e1212
Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, Lin L (2020) Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun 11(1):1–12
Jamil MD, Waheed M, Akhtar S, Bangash N, Chaudhari SK, Majeed M, Hussain M, Ali K, Jones DA (2022) Invasive plants diversity, ecological status, and distribution pattern in relation to edaphic factors in different habitat types of district Mandi Bahauddin, Punjab, Pakistan. Sustainability (Switzerland) 14:20
Jeffery IB, O'Toole PW, Öhman L, Claesson MJ, Deane J, Quigley EM, Simrén M (2012) An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut 61(7):997–1006
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL (2000) The large-scale organization of metabolic networks. Nature 407(6804):651–654. https://doi.org/10.1038/35036627
Kamel Boulos MN, Resch B, Crowley DN, Breslin JG, Sohn G, Burtner R, Lu Z (2011) Crowdsourcing, citizen sensing and sensor web technologies for public and environmental health surveillance and crisis management: trends, OGC standards and application examples. Int J Health Geogr 10(1):67. https://doi.org/10.1186/1476-072X-10-67
Karstens L, Asquith M, Davin S, Fair DA, Gregory WT, Wolfe AJ, McWeeney SK (2019) Controlling for contaminants in low-biomass 16S rRNA gene sequencing experiments. mSystems 4(4):e00290–e00219
Khan AM, Li Q, Saqib Z, Khan N, Habib T, Khalid N, Majeed M, Tariq A (2022) MaxEnt modelling and impact of climate change on habitat suitability variations of economically important Chilgoza pine (Pinus gerardiana wall.) in South Asia. Forests 13:5
Khoja AA, Haq SM, Majeed M, Hassan M, Waheed M, Yaqoob U, Bussmann RW, Alataway A, Dewidar AZ, Al-Yafrsi M, Elansary HO, Yessoufou K, Zaman W (2022) Diversity, ecological and traditional knowledge of pteridophytes in the Western Himalayas. Diversity 14:8
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Flores R (2018) Best practices for analysing microbiomes. Nat Rev Microbiol 16(7):410–422
Lam TB, Hultcrantz M, Wallis C et al (2022) Robot-assisted radical prostatectomy versus open radical prostatectomy: a systematic review and meta-analysis. Eur Urol 17:2617–2631. https://doi.org/10.1016/j.eururo.2022.01.057
Laxminarayan R, Duse A, Wattal C, Zaidi AK, Wertheim HF, Sumpradit N, Cars O (2013) Antibiotic resistance—the need for global solutions. Lancet Infect Dis 13(12):1057–1098. https://doi.org/10.1016/S1473-3099(13)70318-9
Lucas TC (2020) A translucent box: interpretable machine learning in ecology. Ecol Monogr 90(4):e01422
Lutgring JD, Machado MJ, Benitez AJ (2020) Evaluation of the VITEK® 2 automated susceptibility testing system against carbapenemase-producing enterobacteriaceae with a modified carbapenem inactivation method. J Clin Microbiol 58(5):e02088–e02019. https://doi.org/10.1128/JCM.02088-19
Majeed M, Bhatti KH, Amjad MS, Abbasi AM, Rashid A, Nawaz F, Ahmad KS (2020a) Ethno-veterinary practices of Poaceae taxa in Punjab, Pakistan
Majeed M, Bhatti KH, Amjad MS, Abbasi M, Id RWB, Nawaz F, Rashid A, Mehmood A, Id MM, Khan WM, Id SA (2020b) Ethno-veterinary uses of Poaceae in Punjab, Pakistan. PLoS One 15:e0241705. https://doi.org/10.1371/journal.pone.0241705
Majeed M, Bhatti KH, Amjad MS (2021a) Impact of climatic variations on the flowering phenology of plant species in Jhelum district, Punjab, Pakistan. Appl Ecol Environ Res 19:5
Majeed M, Bhatti KH, Pieroni A, Sõukand R, Bussmann RW, Khan AM, Chaudhari SK, Aziz MA, Amjad MS (2021b) Gathered wild food plants among diverse religious groups in Jhelum District, Punjab, Pakistan. Foods 10:3
Majeed M, Tariq A, Anwar MM, Khan AM, Arshad F, Mumtaz F, Farhan M, Zhang L, Zafar A, Aziz M, Abbasi S, Rahman G, Hussain S, Waheed M, Fatima K, Shaukat S (2021c) Monitoring of land use? And cover change and potential causal factors of climate change in Jhelum District, Punjab, Pakistan, through GIS and multi-temporal satellite data. Land 10:10
Majeed M, Lu L, Haq SM, Waheed M, Sahito HA, Fatima S, Aziz R, Bussmann RW, Tariq A, Ullah I, Aslam M (2022a) Spatiotemporal distribution patterns of climbers along an abiotic gradient in Jhelum District, Punjab, Pakistan. Forests 13:8
Majeed M, Tariq A, Haq SM, Waheed M, Anwar MM, Li Q, Aslam M, Abbasi S, Mousa BG, Jamil A (2022b) A detailed ecological exploration of the distribution patterns of wild Poaceae from the Jhelum District (Punjab), Pakistan. Sustainability (Switzerland) 14:7
Majeed M, Lu L, Anwar MM, Tariq A, Qin S, El-Hefnawy ME, El-Sharnouby M, Li Q, Alasmari A (2023) Prediction of flash flood susceptibility using integrating analytic hierarchy process (AHP) and frequency ratio (FR) algorithms. Front Environ Sci 10:1037547. https://doi.org/10.3389/fenvs.2022.1037547
Matchado MS et al (2021) Network analysis methods for studying microbial communities: a mini review. Comput Struct Biotechnol J 19:2687–2698. https://doi.org/10.1016/j.csbj.2021.05.001
Nebert DW, Zhang G, Vesell ES, Dixon K (2020) The human cytochrome P450 (CYP) allele nomenclature database: a one-stop site for nomenclature, functional-allelic-variant reference, and genotype–phenotype relations. Hum Genomics 14(1)
Pasolli E, Asnicar F, Manara S et al (2019) Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176(3):649–662
Qu K, Guo F, Liu X, Lin Y, Zou Q (2019) Application of machine learning in microbiology. Front Microbiol 10:827
Ribeiro MT, Singh S, Guestrin C (2016) “Why should I trust you?” Explaining the predictions of any classifier. In: Proceedings of the 22nd ACM SIGKDD international conference on knowledge discovery and data mining, pp 1135–1144
Sahayasheela VJ, Lankadasari MB, Dan VM, Dastager SG, Pandian GN, Sugiyama H (2022) Artificial intelligence in microbial natural product drug discovery: current and emerging role. Nat Prod Rep 39:2215
Sharma A, Gupta A, Patel D et al (2022) Machine learning-driven metabolic engineering for enhanced secondary metabolite production in streptomyces. 3 Biotech 12:449
Sinha D, Maurya AK, Abdi G, Majeed M, Agarwal R, Mukherjee R, Ganguly S, Aziz R, Bhatia M, Majgaonkar A, Seal S, Das M, Banerjee S, Chowdhury S, Adeyemi SB, Chen JT (2023) Integrated genomic selection for accelerating breeding programs of climate-smart cereals. Genes 14:7
Smith J, Brown L, Garcia M et al (2022) Integrating artificial intelligence for enhanced bioremediation of industrial contaminated sites. Environ Sci Eng 5:100016
Tang H, Zhao X, Dube L, Boudreau RA, Fang R, Xu L (2021) An integrated smartphone-based platform for rapid antimicrobial susceptibility testing. Adv Sci 8(18):2101407. https://doi.org/10.1002/advs.202101407
Tassadduq SS, Akhtar S, Waheed M, Bangash N, Nayab DE, Majeed M, Abbasi S, Muhammad M, Alataway A, Dewidar AZ, Elansary HO, Yessoufou K (2022) Ecological distribution patterns of wild grasses and abiotic factors. Sustainability (Switzerland) 14:18
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Knight R (2017) A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551(7681):457–463
Tirtawijaya G, Meinita MDN, Marhaeni B, Haque MN, Moon IS, Hong Y-K (2018) Neurotrophic activity of the Carrageenophyte Kappaphycus alvarezii cultivated at different depths and for different growth periods in various areas of Indonesia. Evid Based Complement Alternat Med 2018:1098076
Ullah I, Aslam B, Shah SHIA, Tariq A, Qin S, Majeed M, Havenith HB (2022) An integrated approach of machine learning, remote sensing, and GIS data for the landslide susceptibility mapping. Land 11:8
Waheed M, Arshad F, Majeed M, Fatima S, Mukhtar N, Aziz R, Mangrio WM, Almohamad H, Dughairi AA, Al-Mutiry M, Abdo HG (2022) Community structure and distribution pattern of woody vegetation in response to soil properties in semi-arid Lowland District Kasur Punjab, Pakistan. Land 11:12
Waheed M, Arshad F, Majeed M, Haq SM, Aziz R, Bussmann RW, Ali K, Subhan F, Jones DA, Zaitouny A (2023) Potential distribution of a noxious weed (Solanum viarum Du-nal), current status, and future invasion risk based on MaxEnt modeling. In: Geology, ecology, and landscapes. Taylor & Francis, p 1. https://doi.org/10.1080/24749508.2023.2179752
Yao M, Liu Z, Hou L et al (2021) Machine learning models for predicting nutrient concentrations and cycling rates in polluted river ecosystems. Glob Biogeochem Cycles 35(9):e2021GB007146
Zhang B, Sun L, Zheng W et al (2021) Machine learning reveals the environmental and management impacts on soil microbial communities in Chinese tea plantations. Environ Microbiol 23(7):3435–3449
Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Jansson JK (2018) Biogeography of the ecosystems of the healthy human body. Genome Biol 19(1):1–14. https://doi.org/10.1186/s13059-018-1556-2
Zmora N, Zilberman-Schapira G, Suez J et al (2018) Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174(6):1388–1405
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Naveed, M. et al. (2024). Use Cases and Future Aspects of Intelligent Techniques in Microbial Data Analysis. In: Khamparia, A., Pandey, B., Pandey, D.K., Gupta, D. (eds) Microbial Data Intelligence and Computational Techniques for Sustainable Computing. Microorganisms for Sustainability, vol 47. Springer, Singapore. https://doi.org/10.1007/978-981-99-9621-6_17
Download citation
DOI: https://doi.org/10.1007/978-981-99-9621-6_17
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-99-9620-9
Online ISBN: 978-981-99-9621-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)