Development of Microbiome Biobanks – Challenges and Opportunities

The microbiome research field is rapidly evolving, but the required biobanking infrastructure currently fragmented and not prepared for of microbiomes. rapid advancement technologies requires an urgent assessment how biobanks can underpin by preserving samples their functional potential. Traditionally, microbiology has relied on culture collections associated services to ensure quality reproducibility microbiological [1.Ryan M.J. et al.Fungal biological resources support international development: challenges opportunities.World J. Microbiol. Biotechnol. 2019; 35: 139Crossref PubMed Scopus (10) Google Scholar]. Microbiome science signals a paradigm shift in scientific approach from preservation axenic towards complex communities, which supporting be developed. EU project MicrobiomeSupport assessed resource needs this important area (Figure 1). In paper we consider why what need preserve, it should research. Microbiomes are dynamic systems consisting bacteria, archaea, fungi, algae, protists, viruses, principles formation/functioning same regardless host organism or environment. A recent revisit definition proposes that theatre activities microorganisms living given ecosystem [2.Berg G. al.Microbiome re-visited: old concepts new challenges.Microbiome. 2020; 8: 103Crossref (245) Whilst every ‘culture collection’ isolated microbiomes, these represent culturable components preserved state. German DSMZ collection one few with broader, collective deposits samples, including strains Arabidopsis [3.Bai Y. al.Functional overlap leaf root microbiota.Nature. 2015; 528: 364-369Crossref (515) Scholar], human intestinal microbiomes [4.Browne H.P. al.Culturing ‘unculturable’ microbiota reveals novel taxa extensive sporulation.Nature. 2016; 533: 543-546Crossref (575) mouse [5.Lagkouvardos I. al.The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity potential gut microbiota.Nat. 1: 16131Crossref (204) Culture typically operate business model where organisms propagated sale distribution. However, only finite supply source, option, although provide ‘mock’, ‘synthetic’, ‘constructed’ microbial consortia control (QC) product supply. Conversely, ‘biobanks’ may contain tissues ‘frozen’ ‘fixed’ as measure ‘snapshot’ time. Various institutes biobank patients' stool future medical use, example, AdvancingBio (USA), OpenBiome Netherlands Donor Faeces Bank (The Netherlands), Metagenopolis (France), HMGU Biobank (Germany). Stool banks leading way through development sample handling processes protocols. This experience will improve available subsequent use translatable scientists working other domains such food agriculture. agricultural domain, Rothamsted Sample Archive (UK) consists wheat grain, straw, soil, herbage together fertilizers. Seed banks, Kew Millennium (UK), seeds endophytes. microbes optimally Scholar] around sustainability ‘growth supply’, generally store necessarily focusing viability stability all constituent components. represents clear demarcation ‘biobank’ archive repository, there occasional exceptions. Microbiota Vault (www.microbiotavault.org) first major step comprehensive resource. initiative proposal vault humans calls effort [6.Bello M.G.D. al.Preserving diversity.Science. 2018; 362: 33-34Crossref (68) immense. Researchers aware unintentionally fundamentally altering functionality integrity microbiome, system changes response environmental influences biotic factors. At level, removal single critical component due application non-optimized storage could irreversibly affect system. Bell [7.Bell T. Next-generation experiments linking community structure functioning.Environ. Rep. 11: 20-22Crossref (13) quoted Adams [8.Adams D. Salmon Doubt: Hitchhiking Galaxy One Last Time. MacMillan, 2002Google ‘If you try take cat apart see works, thing have your hands nonworking cat’, issue when endeavoring conserve sample. How would distinguish ‘whisker’ ‘heart’ assess does its relationship total whole system? For very nature crop-related crop variety, management practices, adds eliminates microbes. When considering two essential questions answered: (i) preserved, (ii) best it? question about preserve controversial one, ultimately serves generation microbiome-sourced products (which also commercial value) allow during time altered practices climate change. Similarly, probiotics remain stable over Sometimes makes sense community, symbionts host, rhizobacteria soil/roots, bacteria even enrichment cultures natural communities [9.Gich F. al.Enrichment previously uncultured adhesion solid surfaces.Environ. 2012; 14: 2984-2997Crossref (17) Preserving genomic DNA studies repeated confirmation results repeatability information ‘snapshot time’ deliver evidence being present indication whether (or was) viable active at sampling. storing RNA transcriptomic assessments were potentially functional. Therefore, respect current state art, nucleic acids, ‘intact’ sample, protein extracts metabolic fractions stored called for. Capacity significant challenge approach. It practical large amounts hence much representative becomes critical. agriculture encompasses thousands localized Indeed, many site-specific temporal true snapshot microbiomes? precision agriculture, moving smaller grids relying field. We calculate us best, most accurate example. Further, time, might drift result processing storage. Genomic was something considered eukaryotic primary cell lines [10.Geraghty R.J. al.Guidelines biomedical research.Br. Cancer. 2014; 111: 1021-1046Crossref (212) With genetic impact species abundance happen faster. fundamental requirement optimize techniques investigate cryobiological alternative approaches applied. requirements delivered advances addressed, preferably targeted coordinated program. Historically, cryopreservation freeze drying been methods choice fungi pure form because they organism, maintaining close original ‘unpreserved’ wild type possible. systems, pathogenicity key traits compromised if suboptimal applied Cryopreservation ‘gold standard’ since 1960s reports samples. Kerckhof al. [11.Kerckhof F.-M. al.Optimized mixed conserved diversity.PLoS One. 9e99517Crossref (47) evaluated protocol methanotrophic coculture, oxygen-limited autotrophic nitrification/denitrification biofilm, fecal material donor, succeeded both (composition taxa) Vekeman Heylen [12.Vekeman B. K. Preservation communities.in: McGenity Hydrocarbon Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, 2015: 299-315Crossref described –80°C ultra-low temperatures. widely accepted that, cryopreserved, freeze-tolerant cells survive. translates multiple cryopreservation, optimally, unintended selective pressures community. aim composition possible originally host. variety metagenomics [13.Mauchline T.H. al.Old meets new: probable number validation metagenomic metatranscriptomic datasets soil.Lett. Appl. 66: 14-18Crossref (2) transcriptomics [14.Bashiardes S. al.Use metatranscriptomics research.Bioinform. Biol. Insights. 10BBI.S34610Crossref (177) used construction functionality. These success regime each limitations. combination approaches, proposed Easterly [15.Easterly C.W. al.metaQuantome: integrated, quantitative metaproteomics connections between taxonomy function microbiomes.Mol. Cell. Proteom. 18: S82-S91Abstract Full Text PDF (15) – who ‘the metaQuantome’ reveal oral forward. least, tests undertaken before preservation/storage order characterize then postpreservation compositional integrity. addressed detail scientific, economic, social, perspectives. Taking consideration complexity across environments, prioritized list agreed upon focus efforts achieve advancements. biggest technological bottleneck optimized methodologies preservations’ terms complementarity necessitates enable work effective support. require identification infrastructural overlaps gauge available/missing within beyond. output MicrobiomeSupport, received funding European Union’s Horizon 2020 Research Innovation Programme under grant agreement No 818116 . Development Biobanks Challenges Opportunities: (Trends , 89–92; 2021)Ryan al.Trends MicrobiologyFebruary 8, 2021In BriefIn printed version article, ‘The Bank’ incorrectly identified ‘Stool East’. online rectified refer Bank’. Full-Text