How do microbial culture collections underpin the microbiome era?

1. How do microbial culture collections underpin the microbiome era? Nelson Lima Micoteca da Universidade do Minho (MUM) CEB-Centre of Biological Engineering University of Minho Braga - Portugal

2. Defining concepts: “Microbes” is a colloquial term for microorganisms, but usually referring to bacteria only by the lay citizens “Microbiota” is a collective term for culture-dependent microorganisms, generally assumed to include taxa of bacteria (eubacteria and archaebacteria), fungi (yeasts and filamentous fungi) and viruses, associated with a particular habitat

3. Lister in 1878 and Kock in 1881 described for the 1st time the pure culture isolation techniques Preservation and distribution of microorganisms appears for the 1st time by the hand of Frantisek Král in 1890 in Prague (Czech Republic) The concept of Culture Collection was born 1886 - Escherich´s isolate (Bacteriumcolicommune) The first isolate of Escherichia coliwas deposited in the National Collection of Type Cultures (strain NCTC 86) in 1920, the year of its creation, by the Lister Institute in London

4. ECCO: Ourdevelopments…. ECCO starts in 4th ICCC, Brno, 1981 Decision to meet annually in different European countries ECCO currently involves 79 corporate members (Culture Collections (CC) /microBiological Resource Centers (mBRCs)) from 26 European countries that hold more than 400 000 strains They store a vital source of type and reference strains for research and industry and a large pool of biodiversity of microorganisms isolated from humans, animals, plants, foodstuffs and the environment Around 20 ECCO member CC are ISO-9000 certified for several activities (preservation, storage, distribution of biological material, etc.) 23 ECCO member CC have been recognized as an IDA under the Budapest Treaty (1977) on the International Recognition of the Deposit of Microorganisms for the purposes of Patent procedure

5. Services provided by ECCO member culture collections: Deposition and long-term maintenance of living biological materials Supply of living, pure, unchanged and authenticated biological materials Modern technologies for the isolation, cultivation, characterisation and identification of living biological materials Access to information on deposits in public databases, that are permanently curated and updated Collection related research Consultancy and training in collection related topics and regulatory issues ... besides CC serve as sources of microorganisms cited in scientific literature that can be used in the confirmation of results (reproducibility in science) and for further accumulative studies (reuse) and biotechnological applications only about 1% of bacteria published in scientific journals are deposited in CC.

6. Customer service needs from ECCO member culture collections:

7. Change the blurry current situation… … meet the needs! services? data? ? ? ? ? ? ? resources? user user user user user user training? access? expertise? Suboptimal exploitation of accessible resources in cc

8. Microbial Resource Research Infrastructure • Will build a pan-European distributed research infrastructure that provides facilitated access to high quality microorganisms, their derivatives, associated data and services for research, development and application • Will connect public resource centres with researchers and policy makers as well as other stakeholders to deliver material and services more effectively and efficiently to meet the needs of innovation in biotechnology

9. MIRRI Integrated Solution

10. MIRRI Integrated Solution: High-Throughput Sequencing (HTS)/Next Generation Sequencing (NGS) “Metagenomics” is the culture-independent genomic analysis of a community of microorganisms An unprecedented scale on microbial knowledge was generated with the unknown (unculturable) microorganisms (OTUs) <=> Viable But Not Culturable (VBNC) Moldenhauer, J. (2018) Learning from clinical microbiologists – culturomics and metagenomics. Eur. Pharma. Rev. 23: 5-7.  Metagenomics gives a partial snapshot of the microbiota and cannot identify if the sequences belong to active or quiescent microorganisms (this latter limitation can be mitigated by metatranscriptomics)

11. MIRRI Integrated Solution: Microbiome & THS/NGS “Microbiome” is a collective term for genomes of commensal microorganisms associated with a particular habitat cattle* cattle** sheep** goat** Rumen Microbiomes *Zehavi, T. et al. (2018) Insights into culturomics of the rumen microbiome. Front. Microbiol. 9:1999.  **Henderson, G. et al. (2015). Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5:14567

12. MIRRI Integrated Solution: Microbiome & Culturomics “Culturomics” => rebirth of cultures What is the portion of the rumen microbiome that can potentially be cultivated? Out of the total 3893 OUTs (orange) defined medium + (green) undefined medium => increase the number of different cultured OTUs by up to 40% Out of the total 2881 OTUs detected in the original rumen sample and its dilutions, 686 (23%) OTUs were also found on the plates. Zehavi T. et al. (2018) Insights into culturomics of the rumen microbiome. Front. Microbiol. 9:1999. 

13. MIRRI Integrated Solution: From OTUs to Culurable Microorganisms Out of 82 cultured bacterial genera, 58 of which do not have isolated representatives in any of the international CC/mBRCs catlle* cattle sheep goat international CC/mBRCs cattle* cultured on plates Rumen Microbiomes Culturable Microorganisms *Zehavi T. et al. (2018) Insights into culturomics of the rumen microbiome. Front. Microbiol. 9:1999. 

14. MIRRI Integrated Solution: From OTUs to Culurable Microorganisms Classification & Preservation Lagier, J.-C. et al. (2016) Culture of previously uncultured members of the human gut microbiota by culturomics. Nature Microbiol. 1:1-8. 

15. Declining human intestinal microbial diversity with industrialization Faecal Microbiota Transplantation (FMT) => a restorative technique for returning ecological balance to the colon diseases Gut microbiota diversity It suspects that the microbes disappearing in urban societies are those that are needed to maintain health and prevent many metabolic, immune, and cognitive diseases Dominguez Bello, M.G. et al. (2018) Preserving microbial diversity. Science 363: 33-34.

16. MIRRI Integrated Solution: the future… Giving microbial diversity a home… …will underpin the microbiome era and foster innovation to develop health, sustainability and bioeconomy

17. Thank you for your attention!!! Slide by Vicent Robert, Westerdijk Institute