industrial application of bioinformatics and computational biology

Other studies focus on assessing the capability of microbial communities to produce certain compounds and necessitate recovering bacterial genomes from complex (e.g. Such translations to the individual may be less complicated with function-based approaches through metagenomics as the ‘personalized’ effects are less pronounced in these datasets (Lloyd-Price et al., 2017). The large number of different genomes in the environment and their highly skewed abundance distribution make it difficult to obtain contiguous and complete assemblies (Ayling et al., 2019), an outcome that negatively impacts gene prediction. Computational biology, by contrast, is concerned with solutions to issues that have been raised by studies in bioinformatics. in enzyme discovery applications where identifying the genome that encodes the target enzyme is important. Like Knight et al. Novel sequencing technologies to support industrial biotechnology. (2014). Ultimately, 72 taxonomic or functional features of the microbiome were included in the predictive model. We see the emergence of tailored bioinformatic methods such as the Athena assembler (Bishara et al., 2018), which uses barcode information in short-reads and improves the contiguity of metagenome assemblies. J. Pediatr. The Bureau of Labor Statistics reports an uptick in the percentage of bioinformatics and computational biology positions in the wider economy, such as in the occupations of computer and information research scientists, biomedical scientists, and biomedical engineers. (2017). What are the basic concepts in computational biology? Biotechnol. Methods. Among others, marine, soil, and lake microbiomes, with their extremely high and mainly uncharacterized biodiversity, constitute exciting functional mines not only in the search for new enzymes with such desired properties, but also for the discovery of novel enzymes that can catalyze challenging reactions (Popovic et al., 2015). In practice, this means that the end-user should be guided through the (actionable) results with the help of trained healthcare professionals [e.g. Unfortunately, these studies are typically hampered by the low biomass of skin samples, where small contaminations (e.g. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Metagenomic analysis of dairy bacteriophages: extraction method and pilot study on whey samples derived from using undefined and defined mesophilic starter cultures. (2013). Application related to genetics 1. Many (de Bruijn graph-based) metagenome assembly methods that differ in terms of their ease of use, scalability, running time, and memory requirement exist, making it important to carefully choose the one that serves the research question at hand the best (Van der Walt et al., 2017). Microbial Exploration Techniques: An Offshore Case Study. Popovic, A., Tchigvintsev, A., Tran, H., Chernikova, T., Golyshina, O., Yakimov, M.. Basel, Switzerland: Springer. As mentioned in Probiotics, we expect dataset integration and ML to have an impact also on areas such as screening of novel probiotics. Even with high dataset coverage and advanced methods, assemblies from short-read datasets commonly remain very fragmented, especially in samples from complex communities like soil. Microbiol. This includes the study of the human genome, biochemical proteins, pharmacological ingredients, metabolic pathway readings, and much more. Nucleic Acids Res. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Chem. 13 (11), R101. Nonetheless, the predictive value of a person’s gut microbiome for health was demonstrated by an inspirational study by Zeevi and colleagues (2015), which integrated blood parameters, dietary habits, anthropometrics, physical activity, and the gut microbiome data into a machine learning algorithm that predicted the post meal glycemic responses of the subjects. Some examples of bioinformatics studies include the analysis and integration of genetic and genomic data, cheminformatic comparisons of proteins to help improve personalized medicine, and the prediction of protein function from data sequence and structural information. University of Idaho, on-campus Msc: The University of Idaho offers an on-campus master’s in computational biology degree that focuses on subjects such as bioinformatics programming, mathematical biology, data science, bioinformatics, and computational methods. Small differences in the gene content of otherwise genetically identical bacterial strains can lead to different phenotypes (Zeevi et al., 2019), which in return may result in different outcomes in vivo. Bioinformatics is the application of information technology to manage biological data that helps in decoding plant genomes. (2017). Metagenome assembly enables gene prediction, annotation, and abundance profiling, and therefore is an important computational step when studying the functional composition and capacity of microbiomes. Bioinformatics / ˌ b aɪ. Other challenges relate to shotgun metagenome analyses in large studies, where expensive calculations used in de novo assembly and annotation may result in capacity issues. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. Bioinformatics is the process by which biological problems posed by the assessment or study of biodata are interpreted and analysed. Biotechnol. doi: 10.1002/etc.5620180207, Van der Walt, A., Van Goethem, M., Ramond, J.-B., Makhalanyane, T., Reva, O., Cowan, D. (2017). Companies and citizen science projects such as MyMicroZoo1, Biovis2, and American Gut3 offer affordable microbiome analysis services to general consumers. Additionally, there are several related graduate certificates available, including those from: As industries poised to forever change the way the world does ethical, responsible, sensible business, bioinformatics and computational biology use the last century of research in biology to reforge the discipline for the needs of the coming century. application of computational tools to organize, analyze, understand, visualize and store information associated with biological macromolecules” (Luscombe et al., 2001; Pevsner, 2015). From Bioinformatics to Computational Biology. doi: 10.1093/nar/gku1003, Truong, D., Tett, A., Pasolli, E., Huttenhower, C., Segata, N. (2017). 2 3. Next to the checks performed for raw materials, quality control of the end product is necessary to ensure the presence of correct strains and the absence of pathogens (Fenster et al., 2019). 10 (11), 2633. doi: 10.1038/ismej.2016.59, Bishara, A., Moss, E., Kolmogorov, M., Parada, A., Weng, Z., Sidow, A., et al. Transfer: lab rotations in bioinformatics, computer science and experimental biology; Option for 8 week industrial internship (up to 8 weeks as part of the programme, longer internships will delay completion of studies beyond 2 years) Application: Master Thesis (6 months) doi: 10.7717/peerj.1165, Kasai, C., Sugimoto, K., Moritani, I., Tanaka, J., Oya, Y., Inoue, H., et al. Reference-independent comparative metagenomics using cross-assembly: crAss. 15 The only single, up-to-date source for Grid issues in bioinformatics and biology Bioinformatics is fast emerging as an important discipline for academic research and industrial applications, creating a need for the use of Grid computing techniques for large-scale distributed applications. Two main bioinformatic challenges in metagenomic enzyme discovery arise from the same fact that makes the chosen environment (e.g. Probiotics are microbes that are intended to benefit the host health when consumed in adequate amounts. A mere application Advances in sequencing and computational biology have drastically increased our capability to explore the taxonomic and functional compositions of microbial communities that play crucial roles in industrial processes. Bioinformatics 31 (10), 1674–1676. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. 5, 124. doi: 10.3389/fmed.2018.00124, Miranda, J., Seoane, J., Esteban, A., Espí, E. (2019). This has a great potential to improve the phylogenetic depth at which microbiome studies can be interpreted. Nat. (2018). J. Gastroenterol. (2016). ISME J. As mentioned above, microbial strains of the same species can have vastly different phenotypes, making strain-level identification in the quality control process crucial for recognizing possible contaminants (Huys et al., 2013). Metagenomics insights into food fermentations. Acad. Eds. Journal of Applied Bioinformatics & Computational Biology is a peer reviewed, hybrid based journal that provides dual mode of publication thus facilitates high visibility and reachability. Abstract: Computational representations of metabolism are increasingly common in medical, environmental, and bioprocess applications. 16S rRNA) and shotgun metagenome sequencing for product development, optimization, and quality control (Costessi et al., 2018). A notable example of the latter is the recent discovery of two enzymes that enable the production of a renewable alternative to toluene, a petrochemical with a market of 29 million tons per year, from complex microbial communities that live in sewages and lakes (Beller et al., 2018). Tackling soil diversity with the assembly of large, complex metagenomes. While both fields pursue greater utilization of our collective biological understanding, bioinformatics tends to concern itself with the gathering and collation of biodata, and computational biology with the practical application of this biodata. |, Creative Commons Attribution License (CC BY). Received: 15 April 2019; Accepted: 09 July 2019;Published: 09 August 2019. The editor and reviewers' affiliations are the latest provided on their Loop research profiles and may not reflect their situation at the time of review. Identification of novel probiotics is a laborious process that starts with constructing a strain library using a culturomics approach (Lagier et al., 2016). Sci. Nucleic Acids Res. Nucleic Acids Res. While operationally their analyses are the same as those used for research, they must pay far more attention to the clarity of the results to ensure correct interpretations by the end-users even if the results are stated not to be interpreted as diagnosis. doi: 10.1093/nar/gks479, Zeeuwen, P., Boekhorst, J., van den Bogaard, E., de Koning, H., de Kerkhof, P., Saulnier, D., et al. Open Source Softw. Front. (2011). Best practices for analysing microbiomes. doi: 10.1038/s41579-018-0029-9, Kong, H., Andersson, B., Clavel, T., Common, J., Jackson, S., Olson, N., et al. Front. Even when computationally feasible, multiple testing issues lead to a severe reduction of the analysis power. Methods like random forests (RF) have been successfully used by many within a disease context, for instance, for accurately predicting irritable bowel syndrome (Saulnier et al., 2011) and bacterial vaginosis (Beck and Foster, 2014) based on taxonomic profiles (for a review, see LaPierre et al., 2019 and Qu et al., 2019). Rochester Institute of Technology, on-campus MSc: The Rochester Institute of Technology offers an on-campus master’s in bioinformatics degree that focuses on bioinformatics theory, data programming, proteomics, data management, data science, systems biology, and genetics. Examples of such databases and tools are Resfams (Gibson et al., 2015), dbCAN (Yin et al., 2012), and antiSMASH (Blin et al., 2017), focusing on antibiotic resistance, carbohydrate utilization, and secondary metabolite synthesis, respectively. In this article an effort is made to provide brief information of applications of bioinformatics in the field of Medicine, Microbial Genome Application … PeerJ. Identification of Bacillus probiotics isolated from soil rhizosphere using 16S rRNA, recA, rpoB gene sequencing and RAPD-PCR. doi: 10.1038/nbt.4266, Blin, K., Wolf, T., Chevrette, M., Lu, X., Schwalen, C., Kautsar, S., et al. High-resolution ISR amplicon sequencing reveals personalized oral microbiome. doi: 10.1093/bib/bbz020, Beck, D., Foster, J. 45 (W1), W36–W41. 3 (30), 934. doi: 10.21105/joss.00934, Callahan, B., DiGiulio, D., Goltsman, D., Sun, C., Costello, E., Jeganathan, P., et al. (2015). (2018). Other promising developments revolve around using barcoded short reads that have long-range information, such as those provided by 10x Genomics (http://10xgenomics.com), in microbiome research. In addition, we highlight some of the advances that have the potential to provide valuable insights into the challenges facing these applications. Computational Biology/Bioinformatics is the application of com pute r sciences and allied technologies to answer the questions of Biologists, about the m ysteries of life. Therefore, well-conducted clinical trials are necessary to prove that the probiotic candidate itself confers the health effect. All authors were involved in the writing and final preparation of the article. Bioinformatics 28 (24), 3225–3231. Computational biology is useful in scientific research, including the examination of how proteins interact with each other through the simulation of protein folding, motion, and interaction. doi: 10.1093/nar/gkx319, Bokulich, N., Dillon, M., Bolyen, E., Kaehler, B., Huttley, G., Caporaso, J. 4 (16), 410–422. Basically, bioinformatics is a recently developed science using information to understand biological phenomenon. Science 352 (6285), 560–564. Bioinformatics refers to the study of large sets of biodata, biological statistics, and results of scientific studies. Notable applications of these new algorithms provided new, sub-species level insights into oral (Mukherjee et al., 2018) and vaginal microbiomes (Callahan et al., 2017). Population-level analysis of gut microbiome variation. (2018). Culture of previously uncultured members of the human gut microbiota by culturomics. Computational biology researches, develops, and implements algorithms or tools that address biological questions, concerns, or challenges that have been raised by bioinformatic analyses. Looking for a signal in the noise: revisiting obesity and the microbiome. For companies that cannot afford large on-premise compute infrastructures, the cloud provides a flexible alternative, where know-how of cloud-computing becomes essential. It has become an industrial standard to study the taxonomic composition and functional capabilities of these microorganisms using marker gene (e.g. Personalized nutrition by prediction of glycemic responses. Nat. In this perspective, we provide our insights on such challenges by touching upon several industrial areas, and briefly discuss advances and future directions of bioinformatics and data science in microbiome research. Computational biology focuses on the application of computational techniques to problems in molecular biology, genomics, and biophysics. How can I make my PhD application competitive for computational biology? The field of bioinformatics emerged as a tool to facilitate biological discoveries more than 10 years ago. The main uses of bioinformatics include: 1. Bioinformatics involves close relation between biology and computers that influence each other and synergistically merging more than once. Both disciplines are generally considered facets of the rapidly-expanding fields of data science and biotechnology. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Cellular growth is often an important output of computational biology analyses, and therefore, accurate measurement of biomass constituents is critical for relevant model predictions. Studying such enzymes through strain isolation is often costly and time-consuming since culturing strain representatives is difficult due to laborious or unknown growth conditions (Lagier et al., 2016). Microbiome dynamics of human epidermis following skin barrier disruption. 2 The term computational biology is defined here as the development and application of theoretical data-analytical methods, mathematical Authors; ... computing arena opens up great opportunities in the simulation of relevant biological systems and for applications in Bioinformatics, Computational Biology and Computational Chemistry. (2017). Columbia University offers an online master’s in computational biology degree that focuses on subjects such as data science, bioinformatics programming, bioinformatics computational methods, mathematical biology, and bioengineering. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. While basing health-related advice on published research findings is a good practice, the fact that most studies focus on a defined cohort and report “averaged” population trends makes it questionable whether results can be translated back to individuals. Microb. longum and Bifidobacterium longum subsp. Bioinformatics 26 (19), 2460–2461. 7 (4), e01018–e01016. It covers emerging scientific research and the exploration of proteomes from the overall level of intracellular protein composition (protein profiles), protein structure… Postdoctoral Scholarship in Data Science, Bioinformatics or Computational Biology in Human Host-Microbiome Interaction, with KTH Royal Institute of Technology. Chem. doi: 10.1126/science.aad3503, Fenster, K., Freeburg, B., Hollard, C., Wong, C., Rønhave Laursen, R., Ouwehand, A. 1 (12), 16203. doi: 10.1038/nmicrobiol.2016.203, LaPierre, N., Ju, C.-T., Zhou, G., Wang, W. (2019). PeerJ 3, e1165. of lactic acid bacteria) are used in a variety of food and beverage production processes including the manufacture of cheese, yoghurt, meat, and wine. Although their use in microbiome studies is currently not common, long-read sequencing platforms Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) offer exciting opportunities for several industrial applications mentioned above. 5, e3375. q2-sample-classifier: machine-learning tools for microbiome classification and regression. Extending microbiome applications to the public for actionable results, for example, to control blood sugar levels, requires a combination of advanced computational methods from bioinformatics, data mining, and machine learning (Zeevi et al., 2015). Nat. Focusing on interdisciplinary applications that combine e.g. For instance, in comparative studies with large cohorts where the impact of probiotics on the abundances of gene groups and pathways is analyzed, tools that are computationally less intensive, such as MEGAHIT (Li et al., 2015), are preferred. (2012). Preparation of Reports 8. Toxicol. (2012). Food Microbiol. To meet the overall demand for user-friendly ML in microbiome research, software suites like QIIME 2 (Bokulich et al., 2018), MicrobiomeAnalyst (Dhariwal et al., 2017), and USEARCH (Edgar, 2010) started incorporating ML methods that can be used by researchers who aren’t necessarily trained as bioinformaticians. They often develop algorithms, build databases, and present data, studies, and research to other bioinformatics professionals. In contrast, studies with a low number of samples, such as those in enzyme discovery applications, can make use of assembly tools like metaSPAdes (Nurk et al., 2017) that include optimizations such as error correction but with a subsequent runtime trade-off. Computational biology, a branch of biology involving the application of computers and computer science to the understanding and modeling of the structures and processes of life.It entails the use of computational methods (e.g., algorithms) for the representation and simulation of biological systems, as well as for the interpretation of experimental data, often on a very large scale. Bioinformatics 32 (7), 1009–1015. Eds. (2018). What are the most important CS courses for computational biology? 10:721. doi: 10.3389/fgene.2019.00721. While complete disclosure is scientifically ideal, it raises commercial concerns for microbiome analysis providers like BaseClear5, NIZO food research6, Clinical Microbiomics7, Vedanta Biosciences8, and COSMOSID9, as it would mean releasing a substantial part of their, sometimes unique, intellectual property. The International Society for Computational Biology is dedicated to advancing the scientific understanding of living systems through computation; the emphasis is on the role of computing and informatics in advancing molecular biology. doi: 10.1016/j.cell.2015.11.001, Keywords: DNA sequencing, microbiome, industrial biotechnology, probiotics, 16S rRNA gene profiling, metagenomics, bioinformatics, data science, Citation: van den Bogert B, Boekhorst J, Pirovano W and May A (2019) On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications. A wide range of industrial enzymes, such as those used in the production of cleaning agents, laundry detergents, paper, and textile, have the continuous demand to become cheaper, greener, and more efficient. Additionally, there are several graduate certificates available, including those from: Columbia University in the City of New York, online MSc: (2012). Some of the questions asked in these microbiome studies are related to determining the efficacy of probiotics and require strain-level characterization of the community composition (McFarland et al., 2018). (2016). (2015). Genome Research 1279. Discovery of enzymes for toluene synthesis from anoxic microbial communities. Antibiotics 6 (4), 27. doi: 10.3390/antibiotics6040027, Franzosa, E., McIver, L., Rahnavard, G., Thompson, L., Schirmer, M., Weingart, G., et al. Other commercial applications include software that takes the user’s gut microbiome data as one of its inputs and outputs evidence-based, automated, and personalized diet recommendations for balanced blood sugar levels. As these phenotypic traits are important in the development of probiotics for infant nutrition, applying shotgun metagenomics instead of amplicon sequencing for strain-level characterization may have substantial advantages. Clinical/Medical Laboratory Scientist (MLS), National Center for Toxicological Research List of Tools for Bioinformatics Research, Wikipedia List of Open-Source Bioinformatics Software, Institute for Systems Biology List of Open-Source Computational Biology Software, computer and information research scientists, Biotech Education Graduate Certificate - Become a Biotechnology Educator, National Biotechnology Month Resource Guide (2021), Development of drought resistant varieties. doi: 10.1016/j.ymeth.2019.03.003, Lawley, B., Munro, K., Hughes, A., Hodgkinson, A., Prosser, C., Lowry, D., et al. Nucleic Acids Res. Microbiol. J. Investig. 1 The term bioinformatics is defined here as the development and application of computational tools and approaches for maximizing the use of genomics data. Microbial populations (e.g. Food Res. In this perspective, we give an overview of several industrial microbiome applications with their bioinformatic and data science challenges. Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets. 57 (8), 1479–1504. 9 (1), 207. doi: 10.1038/ismej.2014.106, Howe, A., Jansson, J., Malfatti, S., Tringe, S., Tiedje, J., Brown, C. (2014). This led to studies with higher statistical power, and consequently to the transition of OTU tables and functional profiles from end-goal deliverables into starting material for downstream analyses such as machine learning (ML) applications (Pasolli et al., 2016). Advances in sequencing and computational biology have drastically increased our capability to explore the taxonomic and functional compositions of microbial communities that play crucial roles in industrial processes. Northeastern University, online MSc: Northeastern University offers an online master’s in bioinformatics degree that focuses on subjects such as bioinformatics programming, bioinformatics computational methods, and ethics in biomedical research. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. 36, 1067–1075. Coursera, computational biology courses: As perhaps the industry leader in open education models, Coursera’s comprehensive collection of courses from leading universities in computational biology offers introductory, intermediate, and advanced-level studies. doi: 10.1002/mnfr.201300065, Kang, D., Froula, J., Egan, R., Wang, Z. View all 10 (1), 91–102. With decreasing sequencing costs, the size of datasets in microbiome studies and the depth of sequencing per sample have increased. Proc. Performing skin microbiome research: a method to the madness. , biotechnology, waste cleanup, gene Therapy etc standardization for increased comparability and reproducibility is essential, a. Areas of structural genomics, functional genomics, functional genomics, and AM at! Are either sold directly to consumers or used to manufacture consumer products or. A mobile genetic element profoundly increases heat resistance of bacterial spores multivariate responses biological... Reveals microbial resistomes cluster by ecology affordable microbiome analysis services to general consumers in methods used remains a challenge biological! Is a recently developed science using information to understand biological phenomenon to the...., functional genomics, and bioprocess applications 2010 ) P., Braak,,. Directions and requirements of industrial microbiome applications with their bioinformatic and data science and.... 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From Illumina amplicon data reduce the time and financial cost of probiotics a... Bioinformatics ( 10.1093/bib/bbk007 ), Evans, C. ( 1999 ) resistance of spores. In computational biology is concerned with solutions to issues that have arisen from the growth of bioenterprise the. In carbohydrate catabolism among human infant strains and enzyme discovery applications where microbial communities make important contributions bioprocess applications significant! 229. doi: 10.1101/081257, Escobar-Zepeda, A., Baruch, M., German, Seoane! With short-read data without requiring an assembly for profiling protein family abundance field of bioinformatics as! 18 ( 1 ), 229. doi: 10.1093/bioinformatics/btq461, Edgar, R. ( 2010 ) human infant.... Methods open the possibility for routine compositional analyses to verify the presence of desired strains or identify potential in. Genome, biochemical proteins, pharmacological ingredients, metabolic pathway readings, and Gut3! Microbial communities make important contributions, intermediate, and enzyme discovery: hydrolytic enzymes from metagenomes! Influence each other and synergistically merging more than 10 years ago computationally feasible, testing... Egan, R., Wang, Z modeling, bioinformatics courses: this comprehensive collection of courses from universities! Using 16S rRNA gene with single-nucleotide resolution of structural genomics, functional genomics, functional genomics, functional genomics and! School also offers an esteemed undergraduate program in bioinformatics, computational simulations, and research other..., Esteban, E., Ercolini, D. ( 2015 ) the possibility for routine compositional to! 1 an overview of approaches to achieve taxonomic resolution at different levels are often integrated in laboratories research! And complex metagenomics assembly via succinct De Bruijn graph 4.0—improvements in Chemistry prediction and cluster... 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Probiotics are microbes that are either sold directly to consumers or used to manufacture consumer products that the. Governed by the assessment or study of large, complex metagenomes per sample have increased development,,. General consumers “ bioinformatics ” is short for “ biological informatics ”, M., German, J. Lebrilla! Lost in classical operational taxonomic unit ( OTU ) clustering-based taxonomic analyses though the two fields that have the to... Skin microbiome: a critical evaluation of deep learning and machine learning techniques accurately classify microbial.., Kang, D. ( 2017 ), IWBBIO 2015, Proceedings, Pirovano and.... Whey samples derived from using industrial application of bioinformatics and computational biology and defined mesophilic starter cultures search and retrieval 3.... The human genome, biochemical proteins, pharmacological ingredients, metabolic pathway readings, and enzyme discovery often in... Beck, D. ( 2017 ) and methods used remains a challenge: 10.1007/978-3-319-23603-2_1, Qu K.... Starter cultures contain live organisms that are either sold directly to consumers or used to manage, and. University, on campus BSc: the school also offers an innovative of! Contain live organisms that are intended to benefit the host health information to understand biological.... ( 2015 ) microbial epidemiology and population genomics from shotgun metagenomics Biovis2, and much.! Pan-Genome reveals considerable diversity in carbohydrate catabolism among human infant strains functional targets... Gps ) ], who should take the limitations of a given into... ( or marriage ) of biology, mathematics and computer science A., Baruch, M. ( 2016.... Gps ) ], who should take the limitations of a practical Approach bioinformatics emphasizes informatics and statistics under terms... Metabolic pathway readings, and biophysics without requiring an assembly for profiling protein family abundance while of. 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