The contribution of microbial biotechnology to sustainable development goals: microbiome therapies

Hindrance to sustainable development: Global inequities, non-progressive education and inadequate science-policy dialogue

Social habits and economies driven by profit are opposing efforts to reach a path of sustainable development. In addition, many communities worldwide have diverged away from nature through consumerism and technology. In the context of the escalating risks and consequences related to global challenges such as the climate crisis and ecosystem degradation, education for sustainable development and science-driven decision-making offer tremendous opportunities for improvement.

Next-Generation Probiotics: Microflora Intervention to Human Diseases

With the development of human genome sequencing and techniques such as intestinal microbial culture and fecal microbial transplantation, newly discovered microorganisms have been isolated, cultured, and researched. Consequently, many beneficial probiotics have emerged as next-generation probiotics (NGPs). Currently, "safety," "individualized treatment," and "internal interaction within the flora" are requirements of a potential NGPs. Furthermore, in the complex ecosystem of humans and microbes, it is challenging to identify the relationship between specific strains, specific flora, and hosts to warrant a therapeutic intervention in case of a disease. Thus, this review focuses on the progress made in NGPs and human health research by elucidating the limitations of traditional probiotics; summarizing the functions and strengths of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides fragilis, Eubacterium hallii, and Roseburia spp. as NGPs; and determining the role of their intervention in treatment of certain diseases. Finally, we aim to provide a reference for developing new probiotics in the future.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

Holdemanella biformis improves glucose tolerance and regulates GLP-1 signaling in obese mice

Impaired glucose homeostasis in obesity is mitigated by enhancing the glucoregulatory actions of glucagon-like peptide 1 (GLP-1), and thus, strategies that improve GLP-1 sensitivity and secretion have therapeutic potential for the treatment of type 2 diabetes. This study shows that Holdemanella biformis, isolated from the feces of a metabolically healthy volunteer, ameliorates hyperglycemia, improves oral glucose tolerance and restores gluconeogenesis and insulin signaling in the liver of obese mice. These effects were associated with the ability of H. biformis to restore GLP-1 levels, enhancing GLP-1 neural signaling in the proximal and distal small intestine and GLP-1 sensitivity of vagal sensory neurons, and to modify the cecal abundance of unsaturated fatty acids and the bacterial species associated with metabolic health. Our findings overall suggest the potential use of H biformis in the management of type 2 diabetes in obesity to optimize the sensitivity and function of the GLP-1 system, through direct and indirect mechanisms.

Microbial Resources, Fermentation and Reduction of Negative Externalities in Food Systems: Patterns toward Sustainability and Resilience

One of the main targets of sustainable development is the reduction of environmental, social, and economic negative externalities associated with the production of foods and beverages. Those externalities occur at different stages of food chains, from the farm to the fork, with deleterious impacts to different extents. Increasing evidence testifies to the potential of microbial-based solutions and fermentative processes as mitigating strategies to reduce negative externalities in food systems. In several cases, innovative solutions might find in situ applications from the farm to the fork, including advances in food matrices by means of tailored fermentative processes. This viewpoint recalls the attention on microbial biotechnologies as a field of bioeconomy and of ‘green’ innovations to improve sustainability and resilience of agri-food systems alleviating environmental, economic, and social undesired externalities. We argue that food scientists could systematically consider the potential of microbes as ‘mitigating agents’ in all research and development activities dealing with fermentation and microbial-based biotechnologies in the agri-food sector. This aims to conciliate process and product innovations with a development respectful of future generations’ needs and with the aptitude of the systems to overcome global challenges.

Metasequencing of V3-V4 Variable Regions of 16S rRNA Gene in Opportunistic Microbiota and Gut Biocenosis in Obese Adolescents

Opportunistic microorganisms in the gut biocenosis were studied in adolescents with normal body weight and obesity (patients consulted at the Clinical Department of Research Center of Family Health and Human Reproduction Problems). The biological material was studied by standard bacteriological methods, representatives of Enterobacteriaceae family were also characterized using metagenomic sequencing of V3-V4 variable regions of 16S gene rRNA. Gut microbiota of obese adolescents was unbalanced and was characterized by low levels of bifido- and lactoflora representatives, a spectrum of E. coli associations, and high prevalence of opportunistic microorganisms and their associations. Representatives of Enterobacteriaceae family were most often found in the gut microbiota of obese adolescents.

Anti-inflammatory and anti-aging effects of chondroitin sulfate

Biological ageing is a process that changes living systems over time, causing impairments in their structure and function. Studying the individual biomarkers of ageing is regarded as the most plausible current theory of age-related inflammatory processes (inflammageing). According to this theory, slightly pronounced chronic aseptic inflammation develops during ageing, which is the basis for the pathogenesis of age-related syndromes and diseases. A key role in implementing different cellular interactions and in regulating the type of an inflammatory response is assigned to the cytokine status (nuclear factor kappa-B (NF-κB), tumor necrosis factor-α (TNF-α), interleukin-1 (IL-1) and IL-6) in an elderly patient with age-related diseases, such as osteoarthritis (OA) and diabetes mellitus (DM), developed in the altered background. Anti-inflammatory drugs include chondroitin sulfate (CS) that, in addition to directly affecting the severity of pain syndrome in OA, also has a modulating effect on the level of systemic inflammation. Pharmaceutical CS plays an important role in tissue remodeling, cell proliferation, migration, and differentiation, apoptosis, activation and deactivation of chemokines and cytokines, by increasing the synthesis of hyaluronic acid and proteoglycans, by suppressing the synthesis of prostaglandin E2 (PGE2), IL-1, and IL-6 and the expression of cytokines and NF-κB. CS belongs to anti-aging drugs.

Evolving trends in next-generation probiotics: a 5W1H perspective

In recent years, scientific community has been gathering increasingly more insight on the dynamics that are at play in metabolic and inflammatory disorders. These rapidly growing conditions are reaching epidemic proportions, bringing clinicians and researcher's new challenges. The specific roles and modulating properties that beneficial/probiotic bacteria hold in the context of the gut ecosystem seem to be key to avert these inflammatory and diet-related disorders. Faecalibacterium prausnitzii, Akkermansia muciniphila and Eubacterium hallii have been identified as candidates for next generation probiotics (NGPs) with exciting potential for the prevention and treatment of such of dysbiosis-associated diseases. The challenges of these non-conventional native gut bacteria lie mainly on their extreme sensitivity to O₂ traces. If these strains are to be used successfully in food, supplements or drugs they need to be stable and active in humans. In the present review, we present an overall perspective of the most updated scientific literature on the newly called NGPs through the 5W1H (What, Why, Who, Where, When, and How) method, an innovative and attractive problem-solving approach that provides the reader an effective understanding of the issue at hand.

Spike-in genomic DNA for validating performance of metagenomics workflows

Shotgun metagenomics is a powerful platform to characterize human microbiomes. However, to translate such survey data into consumer-relevant products or services, it is critical to have a robust metagenomics workflow. We present a tool – spike-in DNA – to assess performance of metagenomics workflows. The spike-in is DNA from two organisms – Alivibrio fischeri and Rhodopseudomonas palustris, in a ratio of 4:1 added to samples before DNA extraction. With a valid workflow, the output ratio of relative abundances of these organisms should be close to 4. This expectation was tested in samples of varying diversities (n = 110), and the mean ratio was 4.73 (99% CI [4.0, 5.24]). We anticipate this tool to be a relevant community resource for assessing the quality of shotgun metagenomics workflows and thereby enable robust characterization of microbiomes.

An Emergy and Decomposition Assessment of China’s Crop Production: Sustainability and Driving Forces

With a growing demand for crop products in China, a great deal of local resources and industrial inputs are consumed including agricultural machineries, chemical fertilizers, pesticides, and energies, which results in many environmental issues such as resource depletion, water pollution, soil erosion and contamination, and CO2 emissions. Thus, this study evaluated the trend of sustainability of China’s crop production from 1997 to 2016 in terms of emergy and further explored the driving forces using decomposition analysis methods. The results showed that the total emergy used (U) increased by 50% from 7.82 × 1023 in 1997 to 1.17 × 1024 solar emergy Joule (sej) in 2016. Meanwhile, the values of the emergy sustainability index (ESI) were all smaller than one with a declining trend year by year, indicating that China’s crop production system is undergoing an unsustainable development pattern. From the results of the ESI decomposition, the renewable resource factor (R/GDP) and land use factor (L/A) are two key factors impeding the sustainable development of the crop production system. Therefore, the increased capacity of renewable resources and enough labor forces engaged in crop production will be the key strategies for its sustainable development.

The DIY Digital Medical Centre

Healthcare systems worldwide are confronted with major economic, organizational and logistical challenges. Historic evolution of health care has led to significant healthcare sector fragmentation, resulting in systemic inefficiencies and suboptimal resource exploitation. To attain a sustainable healthcare model, fundamental, system-wide improvements that effectively network, and ensure fulfilment of potential synergies between sectors, and include and facilitate coherent strategic planning and organisation of healthcare infrastructure are needed. Critically, they must be specifically designed to sustainably achieve peak performance within the current policy environment for cost-control, and efficiency and quality improvement for service delivery. We propose creation of a new healthcare cluster, to be embedded in existing healthcare systems. It consists of (i) local 24/7 walk-in virtually autonomous do-it-yourself Digital Medical Centres performing routine diagnosis, monitoring, prevention, treatment and standardized documentation and health outcome assessment/reporting, which are online interfaced with (ii) regional 24/7 eClinician Centres providing on-demand clinical supervision/assistance to Digital Medical Centre patients. Both of these are, in turn, online interfaced with (iii) the National Clinical Informatics Centre, which houses the national patient data centre (cloud) and data analysis units that conduct patient- and population-level, personalized and predictive(-medicine) intervention optimization analyses. The National Clinical Informatics Centre also interfaces with biomedical research and prioritizes and accelerates the translation of new discoveries into clinical practice. The associated Health Policy Innovation and Evaluation Centre rapidly integrates new findings with health policy/regulatory discussions. This new cluster would synergistically link all health system components in a circular format, enable not only access by all arms of the health service to latest patient data, but also automatic algorithm analysis and prediction of clinical development of individual patients, reduce bureaucratic burden on medical professionals by enabling a greater level of focus of their expertise on non-routine medical tasks, lead to automatic translation of aggregate patient data/new knowledge into medical practice, and orient future evolution of health systems towards greater cohesion/integration and hence efficiency. A central plank of the proposed concept is increased emphasis on reduction of disease incidence and severity, to diminish both patient suffering and treatment costs. This will be achieved at the individual and population levels, through (i) significantly improved access to medical services, (ii) stronger focus on primary and secondary prevention and early treatment measures, and disease susceptibility prediction via personalized medicine, involving inter alia genome analysis at birth and periodic analysis of microbiomes and biomarkers, and integration with other patient health and epidemiology parameters, (iii) improved surveillance and (iv) intervention outcome benchmarking. The dMCs will become drivers of innovation and integrative evolution in health systems, of disease reduction and efficiency gains, and thus major contributors to development of sustainability of health care.

The contribution of microbial biotechnology to sustainable development goals: microbiome therapies

Complex communities of microbes live on and in plants, humans and other animals. These communities are collectively referred to as the microbiota or microbiome. Plants and animals evolved to co-exist with these microbes. In mammals, particular kinds of alteration of the microbiome (dysbiosis) are associated with loss of health, most likely due to loss of microbial metabolites, signalling molecules, or regulators of host pathways. Modern life-style diseases such as Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), type 2 diabetes, obesity and metabolic syndrome have been linked to dysbiosis. These multifactorial diseases involve multiple risk factors and triggers, depletion of certain gut microbiota species being one of them. Live Biotherapeutics operate by restoring microbial products or activities in affected subjects. They are being developed as adjuncts, alternatives or new treatment options for diseases that affect a growing proportion of global citizens.