Calling for a systems approach in microbiome research and innovation

Meisner, Annelein; Wepner, Beatrix; Kostić, Tanja; Overbeek, L.S. van; Bunthof, C.J.; Souza, Rafael Soares Correa de; Olivares, Marta; Sanz, Yolanda; Lange, Lene; Fischer, Doreen; Sessitsch, Angela; Smidt, Hauke

doi:10.1016/j.copbio.2021.08.003

Cited by 23 publications

(25 citation statements)

References 45 publications

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“…With findings in the past decade shedding new light on the role of the microbiome impacting human health, this has become a “new organ” for targeting innovative therapeutic interventions with a promising future market ( 8 , 157 , 158 ). The recent decade has seen rapid growth of microbiome-based projects in academia and biotech companies focusing mainly on gut bacteria.…”

Section: Pharmacological Significance and Therapeutic Innovationsmentioning

confidence: 99%

Microbial metabolites: cause or consequence in gastrointestinal disease?

Fobofou

Savidge

2022

American Journal of Physiology-Gastrointestinal and Liver Physi

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Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancers, metabolic disorders, opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiologic host-microbiome interactions. Generally, in order to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short chain fatty acids, polysaccharides and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthetized by microbial biosynthetic gene clusters. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.

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Section: Pharmacological Significance and Therapeutic Innovationsmentioning

confidence: 99%

Microbial metabolites: cause or consequence in gastrointestinal disease?

Fobofou

Savidge

2022

American Journal of Physiology-Gastrointestinal and Liver Physi

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“…Metagenomics is also considered the primary technique for studying phylogeny and taxonomy of complex microbiomes (Berg et al 2020 ). Microbiome research has evolved rapidly over the past few years however their phylogeny and taxonomy are more complex and less studied (Meisner et al 2022 ) . The use of metagenomics has significantly enhanced understanding on metabolic, physiological and ecological roles of environmental microorganisms (Strazzulli et al 2017 ).…”

Section: Metagenomicsmentioning

confidence: 99%

“…Furthermore, the introduction of new sequencing technologies and protocols has led to numerous new methodologies that negatively affect results of the analyses. There are several specific marker/target genes that have been identified for studying microbiome (Meisner et al 2022 ). These marker genes are functionally conserved across phylogenetic distances thus serving as a molecular clock for studying evolutionary changes.…”

Section: Metagenomicsmentioning

confidence: 99%

Characterization of symbiotic and nitrogen fixing bacteria

Kawaka

2022

AMB Expr

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Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments.

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“…The European-funded coordination and support action MicrobiomeSupport 2 acts by setting a basis for a common R&D framework for food system microbiomes. To achieve this, MicrobiomeSupport conducted mapping exercises ( Meisner et al, 2022 ), proposed common terminology and standards ( Berg et al, 2020 ; Ryan et al, 2021 ) and is developing recommendations for a strategic research and innovation agenda. Microbiomes are an integral component of many scientific fields related to the agrifood system, such as medical, nutrition, feed and food, veterinary, and environmental sciences.…”

Section: Introductionmentioning

confidence: 99%

“…The second biggest thematic cluster comprises publications on soil and plant microorganisms, and research projects on environmental (mostly soil) and plant microbiomes and also projects on primary production systems (mostly agriculture). Within the research projects targeting microbiomes in food products and processing environments, microbiomes used as additives or health supplements and microbiomes of fermented foods (such as starters or ripening cultures) are the most investigated fields ( Meisner et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

et al. 2022

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Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

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Calling for a systems approach in microbiome research and innovation

Cited by 23 publications

References 45 publications

Microbial metabolites: cause or consequence in gastrointestinal disease?

Microbial metabolites: cause or consequence in gastrointestinal disease?

Characterization of symbiotic and nitrogen fixing bacteria

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

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