Abstract
Microbes are mediators in almost all ecosystem processes and act as a pivotal game changer in various ecological activities, globally. Therefore, understanding of microbial community structure and related functions in different environmental and micro-environmental niches is not only critical, but also a matter of greatest importance. Due to our inability to cultivate and preserve all sorts of microorganisms, we are losing some ecologically and industrially relevant components of microbial community, due to extinction caused by environmental and climatic variations with time. Intact sample and microbiome preservation are crucial for future cultivation as well as to study the effects of ecological and climatic variations on community functionality and shift with time, using OMICS. Although, methods for pure culture preservation are almost optimized, the techniques of microbiome preservation still remain as an unsolved challenge for microbiologists due to technical and physiological constraints. Present article discusses, recent approaches of microbial preservation with special reference to intact sample, mixed culture and microbiome preservation. It also incorporates recent practices used to achieve the highest viability and metabolic activities in long-term preserved microbiome.
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Beardsley T (2016) Metagenomic reveals microbial diversity. Bioscience 56:192–196. https://doi.org/10.1641/0006-3568(2006)056[0192:MRMD]2.0.CO;2
Berdy J (2005) Bioactive microbial metabolites. J Antibiot 58:1–26. https://doi.org/10.1038/ja.2005.1
Singh BP, Rateb M, Rodriguez-Couto S, Polizeli MD, Li WJ (2019) Microbial secondary metabolites: recent developments and technological challenges. Front Microbiol 914:1–2. https://doi.org/10.3389/fmicb.2019.00914
O’Brien J, Wright GD (2011) An ecological perspective of microbial secondary metabolism. Curr Opin Biotechnol 22:552–558. https://doi.org/10.1016/j.copbio.2011.03.010
Prakash O, Shouche YS, Jangid K (2013) Microbial cultivation and the role of microbial resource centers in the omics era. Appl Microbiol Biotechnol 53:247–252. https://doi.org/10.1007/s00253-012-4533-y
Prakash O, Nimonkar Y, Shouche YS (2013) Practice and prospects of microbial preservation. FEMS Microbiol Lett 339:1–9. https://doi.org/10.1111/1574-6968.12034
Keswani C, Prakash O, Bharti N, Vílcheze JI, Sansinenea E, Lally RD, Borrissh R, Singh SP, Gupta VK, Fraceto LF, Limak R, Singh HB (2019) Re-addressing the biosafety issues of plant growth promoting rhizobacteria. Sci Total Environ 690:841–852
Lemos LN, Fulthorpe RR, Triplett EW, Roesch LF (2011) Rethinking microbial diversity analysis in the high throughput sequencing era. J Microbiol Methods 86:42–51. https://doi.org/10.1016/j.mimet.2011.03.014
Alonso S (2016) Novel preservation techniques for microbial cultures. In: Ojha K, Tiwari S, Brijesh K (eds) Novel food fermentation technologies, 1st edn. Springer, Cham, pp 7–33. https://doi.org/10.1007/978-3-319-42457-6
Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Bushman FD (2010) Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 10:206. https://doi.org/10.1186/1471-2180-10-206
West AG, Waite DW, Deines P, Bourne DG, Digby A, McKenzie VJ, Taylor MW (2019) The microbiome in threatened species conservation. Biol Conserv 229:85–98
Bodelier P (2011) Toward understanding, managing, and protecting microbial ecosystems. Front Microbiol 80:1–8. https://doi.org/10.3389/fmicb.2011.00080
Blaser MJ, Falkow S (2009) What are the consequences of the disappearing human microbiota? Nat Rev Microbiol 12:887–894. https://doi.org/10.1038/nrmicro2245
Fraher MH, O’toole PW, Quigley EM (2012) Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol 9:312. https://doi.org/10.1038/nrgastro.2012.44
Bello MG, Knight R, Gilbert JA, Blaser MJ (2018) Preserving microbial diversity. Science 362:33–34. https://doi.org/10.1126/science.aau8816
Terveer EM, van Beurden YH, Goorhuis A, Seegers JF, Bauer MP, van Nood E, Dijkgraaf MG, Mulder CJ, Vandenbroucke-Grauls CM, Verspaget HW, Keller JJ (2017) How to: establish and run a stool bank. Clin Microbiol Infect 23:924–930. https://doi.org/10.1016/j.cmi.2017.05.015
Baral B, Akhgari A, Metsä-Ketelä M (2018) Activation of microbial secondary metabolic pathways: avenues and challenges. Synth Syst Biotechnol 3:163–178. https://doi.org/10.1016/j.synbio.2018.09.001
Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett 309:1–7. https://doi.org/10.1111/j.1574-6968.2010.02000.x
Singh AK, Sisodia A, Sisodia V, Padhi M (2019) Role of microbes in restoration ecology and ecosystem services. In: Singh JS, Singh DP (eds) New and future developments in microbial biotechnology and bioengineering, 1st edn. Elsevier, Amsterdam, pp 57–68. https://doi.org/10.1016/B978-0-444-64191-5.00004-3
Dubey A, Malla MA, Khan F, Chowdhary K, Yadav S, Kumar A, Sharma S, Khare PK, Khan ML (2019) Soil microbiome: a key player for conservation of soil health under changing climate. Biodivers Conserv 28:2405–2429. https://doi.org/10.1007/s10531-019-01760-5
Dolfing J, Vos A, Bloem J, Ehlert PAI, Naumova NB, Kuikman PJ (2004) Microbial diversity in archived soils. Science 306:813–813. https://doi.org/10.1126/science.306.5697.813a
Klammer S, Mondini C, Insam H (2005) Microbial community fingerprints of composts stored under different conditions. Ann Microbiol 55:299–305
Roesch LF, Casella G, Simell O, Krischer J, Wasserfall CH, Schatz D, Atkinson MA, Neu J, Triplett EW (2009) Influence of fecal sample storage on bacterial community diversity. Open Microbiol J 3:40–46. https://doi.org/10.2174/1874285800903010040
Tzeneva VA, Salles JF, Naumova N, de Vos WM, Kuikman PJ, Dolfing J, Smidt H (2009) Effect of soil sample preservation, compared to the effect of other environmental variables on bacterial and eukaryotic diversity. Res Microbiol 160:89–98. https://doi.org/10.1016/j.resmic.2008.12.001
Ott SJ, Musfeldt M, Timmis KN, Hampe J, Wenderoth DF, Schreiber S (2004) In vitro alterations of intestinal bacterial microbiota in fecal samples during storage. Diagn Microbiol Infect Dis 50:237–245. https://doi.org/10.1016/j.diagmicrobio.2004.08.012
Nechvatal JM, Ram JL, Basson MD, Namprachan P, Niec SR, Badsha KZ, Matherly LH, Majumdar AP, Kato I (2008) Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J Microbiol Methods 72:124–132. https://doi.org/10.1016/j.mimet.2007.11.007
Song SJ, Amir A, Metcalf L, Amato KR, Xu ZZ, Humphrey G, Knight R (2016) Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems. https://doi.org/10.1128/mSystems.00021-16
Blekhman R, Tang K, Archie EA, Barreiro LB, Johnson ZP, Wilson ME, Tung J (2016) Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Sci Rep 6:31519. https://doi.org/10.1038/srep31519
Choo JM, Leong LE, Rogers GB (2015) Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep 5:16350. https://doi.org/10.1038/srep16350
Dominianni C, Wu J, Hayes RB, Ahn J (2014) Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol 14:103. https://doi.org/10.1186/1471-2180-14-103
Hill CJ, Brown JR, Lynch DB, Jeffery IB, Ryan CA, Ross RP, O’Toole PW (2016) Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. Microbiome 4:19. https://doi.org/10.1186/s40168-016-0164-3
Kerckhof FM, Courtens EN, Geirnaert A, Hoefman S, Ho A, Vilchez-Vargas R, Boon N (2014) Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity. PLoS One 9:e99517. https://doi.org/10.1371/journal.pone.0099517
McKain N, Genc B, Snelling TJ, Wallace RJ (2013) Differential recovery of bacterial and archaeal 16S rRNA genes from ruminal digesta in response to glycerol as cryoprotectant. J Microbiol Methods 95:381–383. https://doi.org/10.1016/j.mimet.2013.10.009
Sinha R, Abnet CC, White O, Knight R, Huttenhower C (2017) The microbiome quality control project: baseline study design and future directions. Genome Biol 16:276. https://doi.org/10.1186/s13059-015-0841-8
Vogtmann E, Chen J, Amir A, Shi J, Abnet CC, Nelson H, Sinha R (2016) Comparison of collection methods for fecal samples in microbiome Studies. Am J Epidemiol 185:115–123. https://doi.org/10.1093/aje/kww177
Wowk B (2012) Electric and magnetic fields in cryopreservation. Cryobiology 64:301–303. https://doi.org/10.1016/j.cryobiol.2012.02.003
Morono Y, Terada T, Yamamoto Y, Xiao N, Hirose T, Sugeno M, Ohwada N, Inagaki F (2015) Intact preservation of environmental samples by freezing under an alternating magnetic field. Environ Microbiol Rep 7:243–251. https://doi.org/10.1111/1758-2229.12238
Braun S, Morono Y, Becker KW, Hinrichs KU, Kjeldsen KU, Jørgensen BB, Lomstein BA (2016) Cellular content of biomolecules in sub-seafloor microbial communities. Geochim Cosmochim Acta 188:330–351. https://doi.org/10.1016/j.gca.2016.06.019
Trembath-Reichert E, Morono Y, Ijiri A, Hoshino T, Dawson KS, Inagaki F, Orphan VJ (2017) Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds. Proc Natl Acad Sci USA 114:9206–9215. https://doi.org/10.1073/pnas.1707525114
Gopal M, Gupta A (2016) Building plant microbiome vault: a future biotechnological resource. Symbiosis 77:1–8. https://doi.org/10.1007/s13199-018-0574-z
Martin-Dejardin F, Ebel B, Lemetais G, Minh HN, Gervais P, Cachon R, Chambin O (2013) A way to follow the viability of encapsulated Bifidobacterium bifidum subjected to a freeze-drying process in order to target the colon: interest of flow cytometry. Eur J Pharm Sci 49:166–174. https://doi.org/10.1016/j.ejps.2013.02.015
Kerckhof FM, Courtens EN, Geirnaert A, Hoefman S, Ho A, Vilchez-Vargas R, Pieper DH, Jauregui R, Vlaeminck SE, Van de Wiele T, Vandamme P (2014) Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity. PLoS One 9:e99517. https://doi.org/10.1371/journal.pone.0099517
DeArmon IA, Orlando MD, Rosenwald AJ, Klein F, Fernelius AL, Lincoln RE, Middaugh PR (1962) Viability and estimation of shelf-life of bacterial populations. Appl Environ Microbiol 10:422–427
Khudyakov AN, Polezhaeva TV, Zaitseva OO, Gűnter EA, Solomina ON, Popeyko OV, Shubakov AA, Vetoshkin KA (2015) The cryoprotectant effect of polysaccharides from plants and microalgae on human white blood cells. Biopreserv Biobank 13:240–246. https://doi.org/10.1089/bio.2014.0077
Martos GI, Minahk CJ, Font de Valdez G, Morero R (2007) Effects of protective agents on membrane fluidity of freeze-dried Lactobacillus delbrueckii ssp. bulgaricus. Lett Appl Microbiol 45:282–288. https://doi.org/10.1111/j.1472-765X.2007.02188.x
Nyanga LK, Nout MJ, Smid EJ, Boekhout T, Zwietering MH (2012) Yeasts preservation: alternatives for lyophilisation. World J Microbiol Biotechnol 28:3239–3244. https://doi.org/10.1007/s11274-012-1118-y
Tymczyszyn EE, Sosa N, Gerbino E, Hugo A, Gómez-Zavaglia A, Schebor C (2012) Effect of physical properties on the stability of Lactobacillus bulgaricus in a freeze-dried galacto-oligosaccharides matrix. Int J Food Microbiol 155:217–221. https://doi.org/10.1016/j.ijfoodmicro.2012.02.008
Santos MI, Gerbino E, Araujo-Andrade C, Tymczyszyn EE, Gómez-ZavagliaA (2014) Stability of freeze-dried Lactobacillus delbrueckii subsp. bulgaricus in the presence of galacto- oligosaccharides and lactulose as determined by near infrared spectroscopy. Food Res Int 59:53–60. https://doi.org/10.1016/j.foodres.2014.01.054
Obara YA, Yamai SH, Nikkawa TA, Shimoda YU, Miyamoto YA (1981) Preservation and transportation of bacteria by a simple gelatin disk method. J Clin Microbiol 14:61–66
Kulkarni GA, Chitte RR (2015) Preservation of thermophilic bacterial spores using filter paper disc techniques. J Bioprocess Biotech 5:1–3. https://doi.org/10.4172/2155-9821.1000223
López-Rubio A, Sanchez E, Wilkanowicz S, Sanz Y, Lagaron JM (2012) Electrospinning as a useful technique for the encapsulation of living bifidobacteria in food hydrocolloids. Food Hydrocolloids 28:159–167. https://doi.org/10.1016/j.foodhyd.2011.12.008
Liu Y, Rafailovich MH, Malal R, Cohn D, Chidambaram D (2009) Engineering of bio-hybrid materials by electrospinning polymer-microbe fibres. Proc Natl Acad Sci USA 106:14201–14206. https://doi.org/10.1073/pnas.0903238106
Woodworth MH, Carpentieri C, Sitchenko KL, Kraft CS (2017) Challenges in fecal donor selection and screening for fecal microbiota transplantation: a review. Gut Microbes 8:225–237. https://doi.org/10.1080/19490976.2017.1286006
Carroll IM, Ringel-Kulka T, Siddle JP, Klaenhammer TR, Ringel Y (2012) Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage. PloS One 7:e46953. https://doi.org/10.1371/journal.pone.0046953
Crowley LC, Scott AP, Marfell BJ, Boughaba JA, Chojnowski G, Waterhouse NJ (2016) Measuring cell death by propidium iodide uptake and flow cytometry. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot087163
Rodríguez-Tobías H, Morales G, Ledezma A, Romero J, Saldívar R, Langlois V, Renard E, Grande D (2016) Electrospinning and electrospraying techniques for designing novel antibacterial poly (3-hydroxybutyrate)/zinc oxide nanofibrous composites. J Mater Sci 51:8593–8609
Bhushani JA, Anandharamakrishnan C (2014) Electrospinning and electrospraying techniques: potential food based applications. Trends Food Sci Technol 38:21–33. https://doi.org/10.1016/j.tifs.2014.03.004
Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J (2017) Practical considerations for large-scale gut microbiome studies. FEMS Microbiol Rev 41:154–167. https://doi.org/10.1093/femsre/fux027
Aguirre M, Eck A, Koenen ME, Savelkoul PH, Budding AE, Venema K (2015) Evaluation of an optimal preparation of human standardized fecal inocula for in vitro fermentation studies. J Microbiol Methods 117:78–84. https://doi.org/10.1016/j.mimet.2015.07.019
Yu C, Reddy AP, Simmons CW, Simmons BA, Singer SW, VanderGheynst JS (2015) Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions. Biotechnol Biofuels 8:206. https://doi.org/10.1186/s13068-015-0392-y
Silkina A, Nelson GD, Bayliss CE, Pooley CL, Day JG (2017) Bioremediation efficacy-comparison of nutrient removal from an anaerobic digest waste-based medium by an algal consortium before and after cryopreservation. J Appl Phycol 29:1331–1341. https://doi.org/10.1007/s10811-017-1066-x
Bircher L, Schwab C, Geirnaert A, Lacroix C (2018) Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology. Microb Biotechnol 11:163–175
Vekeman B, Heylen K (2015) Preservation of microbial pure cultures and mixed communities. Hydrocarb Lipid Microbiol Protoc. https://doi.org/10.1007/8623_2015_51
Fuertez J, Córdoba G, McLennan JD, Adams DJ, Sparks TD (2018) Potential application of developed methanogenic microbial consortia for coal biogasification. Int J Coal Geol 188:165–180. https://doi.org/10.1016/j.coal.2018.02.013
Gaci N, Chaudhary PP, Tottey W, Alric M, Brugère JF (2017) Functional amplification and preservation of human gut microbiota. Microb Ecol Health Dis 28:1–10. https://doi.org/10.1080/16512235.2017.1308070
Lee KM, Adams M, Klassen JL (2019) Evaluation of DESS as a storage medium for microbial community analysis. Peer J 7:e6414. https://doi.org/10.7717/peerj.6414
Bircher L, Geirnaert A, Hammes F, Lacroix C, Schwab C (2018) Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes. Microb Biotechnol 11:721–733. https://doi.org/10.1111/1751-7915.13265
Yarberry A, Lansing S, Luckarift H, Diltz R, Mulbry W, Yarwood S (2019) Effect of anaerobic digester inoculum preservation via lyophilization on methane recovery. Waste Manag 87:62–70. https://doi.org/10.1016/j.wasman.2019.01.033
Tatangelo V, Franzetti A, Gandolfi I, Bestetti G, Ambrosini R (2014) Effect of preservation method on the assessment of bacterial community structure in soil and water samples. FEMS Microbiol Lett 356:32–38. https://doi.org/10.1111/1574-6968.12475
Shaw AG, Sim K, Powell E, Cornwell E, Cramer T, McClure ZE, Li MS, Kroll JS (2016) Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? Microbiome 4:1–14. https://doi.org/10.1186/s40168-016-0186-x
Tap J, Cools-Portier S, Pavan S, Druesne A, Öhman L, Törnblom H, Simren M, Derrien M (2019) Effects of the long-term storage of human fecal microbiota samples collected in RNA later. Sci Rep 9:1–9. https://doi.org/10.1038/s41598-018-36953-5
Tedjo DI, Jonkers DM, Savelkoul PH, Masclee AA, van Best N, Pierik MJ, Penders J (2015) The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects. PloS One 10:e0126685. https://doi.org/10.1371/journal.pone.0126685
Acknowledgements
This work was supported from the Grant No. BT/PR13969/BCE/8/1142/2015, Department of Biotechnology (DBT), Govt. of India. Dhananjay Desai acknowledges principal investigator (AICRP-ADMAS) and Director, ICAR-CCARI Ela, Old Goa, Goa 403402 for permitting him to work on the manuscript. We acknowledge the critical editing of manuscript by Manali Vaijanapurkar.
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Prakash, O., Nimonkar, Y. & Desai, D. A Recent Overview of Microbes and Microbiome Preservation. Indian J Microbiol 60, 297–309 (2020). https://doi.org/10.1007/s12088-020-00880-9
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DOI: https://doi.org/10.1007/s12088-020-00880-9