On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications

Food systems microbiome-related educational needs

Within the European-funded Coordination and Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), the Workshop 'Education in Food Systems Microbiome Related Sciences: Needs for Universities, Industry and Public Health Systems' brought together over 70 researchers, public health and industry partners from all over the world to work on elaborating microbiome-related educational needs in food systems. This publication provides a summary of discussions held during and after the workshop and the resulting recommendations.

Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.

Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.

Current Perspectives and Potential of Probiotics to Limit Foodborne Campylobacter in Poultry

Poultry has been one of the major contributors of Campylobacter related human foodborne illness. Numerous interventions have been applied to limit Campylobacter colonization in poultry at the farm level, but other strategies are under investigation to achieve more efficient control. Probiotics are viable microbial cultures that can establish in the gastrointestinal tract (GIT) of the host animal and elicit health and nutrition benefits. In addition, the early establishment of probiotics in the GIT can serve as a barrier to foodborne pathogen colonization. Thus, probiotics are a potential feed additive for reducing and eliminating the colonization of Campylobacter in the GIT of poultry. Screening probiotic candidates is laborious and time-consuming, requiring several tests and validations both in vitro and in vivo. The selected probiotic candidate should possess the desired physiological characteristics and anti-Campylobacter effects. Probiotics that limit Campylobacter colonization in the GIT rely on different mechanistic strategies such as competitive exclusion, antagonism, and immunomodulation. Although numerous research efforts have been made, the application of Campylobacter limiting probiotics used in poultry remains somewhat elusive. This review summarizes current research progress on identifying and developing probiotics against Campylobacter and presenting possible directions for future research efforts.

Probiotic triangle of success; strain production, clinical studies and product development

The successful development of probiotic foods and dietary supplements rests on three pillars; each with their specific challenges and opportunities. First, strain production; this depends on selecting the right strain with promising technological properties and safety profile. Further the manufacturing of the strain in a stable format at sufficiently high yield, following regulatory and customer requirements on culture media ingredients and other processing aids. The second pillar are the preclinical and clinical studies to document that the strain is a probiotic and exerts a health benefit on the host, the consumer. Especially when aiming for a regulator approved health claim, clinical studies need to be thoroughly performed; following appropriate ethical, scientific and regulatory guidelines. Finally, the probiotic will need to be incorporated in a product that can be brought to the consumer; a dietary supplement or a functional food. Because of the live nature of probiotics, specific challenges may need to be dealt with. Although experience from other strains is helpful in the process, the development is strain specific. Commercialisation and marketing of probiotics are strictly but differently regulated in most jurisdictions; defining what can and cannot be claimed.

Gut microbiome, big data and machine learning to promote precision medicine for cancer

The gut microbiome has been implicated in cancer in several ways, as specific microbial signatures are known to promote cancer development and influence safety, tolerability and efficacy of therapies. The 'omics' technologies used for microbiome analysis continuously evolve and, although much of the research is still at an early stage, large-scale datasets of ever increasing size and complexity are being produced. However, there are varying levels of difficulty in realizing the full potential of these new tools, which limit our ability to critically analyse much of the available data. In this Perspective, we provide a brief overview on the role of gut microbiome in cancer and focus on the need, role and limitations of a machine learning-driven approach to analyse large amounts of complex health-care information in the era of big data. We also discuss the potential application of microbiome-based big data aimed at promoting precision medicine in cancer.

Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application

The scientific community currently defines the human microbiome as all the bacteria, viruses, fungi, archaea, and eukaryotes that occupy the human body. When considering the variable locations, composition, diversity, and abundance of our microbial symbionts, the sheer volume of microorganisms reaches hundreds of trillions. With the onset of next generation sequencing (NGS), also known as high-throughput sequencing (HTS) technologies, the barriers to studying the human microbiome lowered significantly, making in-depth microbiome research accessible. Certain locations on the human body, such as the gastrointestinal, oral, nasal, and skin microbiomes have been heavily studied through community-focused projects like the Human Microbiome Project (HMP). In particular, the gastrointestinal microbiome (GM) has received significant attention due to links to neurological, immunological, and metabolic diseases, as well as cancer. Though HTS technologies allow deeper exploration of the GM, data informing the functional characteristics of microbiota and resulting effects on human function or disease are still sparse. This void is compounded by microbiome variability observed among humans through factors like genetics, environment, diet, metabolic activity, and even exercise; making GM research inherently difficult to study. This chapter describes an interdisciplinary approach to GM research with the goal of mitigating the hindrances of translating findings into a clinical setting. By applying tools and knowledge from microbiology, metagenomics, bioinformatics, machine learning, predictive modeling, and clinical study data from children with treatment-resistant epilepsy, we describe a proof-of-concept approach to clinical translation and precision application of GM research.

Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies

Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.