Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old

Overview

Journal Microbes Environ

Specialty Environmental Health

Date 2019 Jun 28

PMID 31243255

Citations 8

Authors

Hideyuki Tamaki

Affiliations

Soon will be listed here.

Citing Articles

Modern microbiology: Embracing complexity through integration across scales.

Eren A, Banfield J Cell. 2024; 187(19):5151-5170.

PMID: 39303684 PMC: 11450119. DOI: 10.1016/j.cell.2024.08.028.

Roseiterribacter gracilis gen. nov., sp. nov., a novel filterable alphaproteobacterium isolated from soil using a gel-filled microwell array device.

Nakai R, Kusada H, Sassa F, Makino A, Morigasaki S, Hayashi H PLoS One. 2024; 19(6):e0304366.

PMID: 38857291 PMC: 11164329. DOI: 10.1371/journal.pone.0304366.

Impacts of Groundwater Pumping on Subterranean Microbial Communities in a Deep Aquifer Associated with an Accretionary Prism.

Iso S, Sato Y, Kimura H Microorganisms. 2024; 12(4).

PMID: 38674625 PMC: 11052133. DOI: 10.3390/microorganisms12040679.

Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants.

Rachmuhl C, Lacroix C, Giorgetti A, Stoffel N, Zimmermann M, Brittenham G BMC Microbiol. 2023; 23(1):174.

PMID: 37403024 PMC: 10318780. DOI: 10.1186/s12866-023-02915-9.

-Based Phytobiotic Enhances Egg Production in Laying Hens through Microbial Composition Changes in Ileum and Cecum.

Rabelo-Ruiz M, Ariza-Romero J, Zurita-Gonzalez M, Martin-Platero A, Banos A, Maqueda M Animals (Basel). 2021; 11(2).

PMID: 33572138 PMC: 7915398. DOI: 10.3390/ani11020448.

References

Nakamura K, Takahashi A, Mori C, Tamaki H, Mochimaru H, Nakamura K . Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field. Int J Syst Evol Microbiol. 2012; 63(Pt 2):715-722. DOI: 10.1099/ijs.0.041681-0. View

. The Integrative Human Microbiome Project. Nature. 2019; 569(7758):641-648. PMC: 6784865. DOI: 10.1038/s41586-019-1238-8. View

Hillman E, Lu H, Yao T, Nakatsu C . Microbial Ecology along the Gastrointestinal Tract. Microbes Environ. 2017; 32(4):300-313. PMC: 5745014. DOI: 10.1264/jsme2.ME17017. View

Nakahara N, Nobu M, Takaki Y, Miyazaki M, Tasumi E, Sakai S . Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi. Int J Syst Evol Microbiol. 2019; 69(4):1185-1194. DOI: 10.1099/ijsem.0.003291. View

Mourad E, Sarhan M, Daanaa H, Abdou M, Morsi A, Abdelfadeel M . Plant Materials are Sustainable Substrates Supporting New Technologies of Plant-Only-Based Culture Media for in vitro Culturing of the Plant Microbiota. Microbes Environ. 2018; 33(1):40-49. PMC: 5877342. DOI: 10.1264/jsme2.ME17135. View

Kusada H, Kameyama K, Meng X, Kamagata Y, Tamaki H . Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice. Sci Rep. 2017; 7(1):18087. PMC: 5741734. DOI: 10.1038/s41598-017-18122-2. View

Mochimaru H, Tamaki H, Katayama T, Imachi H, Sakata S, Kamagata Y . Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field. Int J Syst Evol Microbiol. 2016; 66(11):4873-4877. DOI: 10.1099/ijsem.0.001444. View

Mouser P, Borton M, Darrah T, Hartsock A, Wrighton K . Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface. FEMS Microbiol Ecol. 2016; 92(11). DOI: 10.1093/femsec/fiw166. View

Nunoura T, Takaki Y, Kazama H, Hirai M, Ashi J, Imachi H . Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing. Microbes Environ. 2012; 27(4):382-90. PMC: 4103545. DOI: 10.1264/jsme2.me12032. View

10.

Chirila F, Tabaran A, Fit N, Nadas G, Mihaiu M, Tabaran F . Concerning Increase in Antimicrobial Resistance in Shiga Toxin-Producing Escherichia coli Isolated from Young Animals during 1980-2016. Microbes Environ. 2017; 32(3):252-259. PMC: 5606695. DOI: 10.1264/jsme2.ME17023. View

11.

Nunoura T, Nishizawa M, Hirai M, Shimamura S, Harnvoravongchai P, Koide O . Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes Environ. 2018; 33(2):186-194. PMC: 6031389. DOI: 10.1264/jsme2.ME17194. View

12.

NandaKafle G, Seale T, Flint T, Nepal M, Venter S, Brozel V . Distribution of Diverse Escherichia coli between Cattle and Pasture. Microbes Environ. 2017; 32(3):226-233. PMC: 5606692. DOI: 10.1264/jsme2.ME17030. View

13.

Hiraoka S, Yang C, Iwasaki W . Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. Microbes Environ. 2016; 31(3):204-12. PMC: 5017796. DOI: 10.1264/jsme2.ME16024. View

14.

Welte C . A microbial route from coal to gas. Science. 2016; 354(6309):184. DOI: 10.1126/science.aai8101. View

15.

Tanaka Y, Matsuzawa H, Tamaki H, Tagawa M, Toyama T, Kamagata Y . Isolation of Novel Bacteria Including Rarely Cultivated Phyla, Acidobacteria and Verrucomicrobia, from the Roots of Emergent Plants by Simple Culturing Method. Microbes Environ. 2017; 32(3):288-292. PMC: 5606700. DOI: 10.1264/jsme2.ME17027. View

16.

Umpierrez A, Bado I, Oliver M, Acquistapace S, Etcheverria A, Padola N . Zoonotic Potential and Antibiotic Resistance of Escherichia coli in Neonatal Calves in Uruguay. Microbes Environ. 2017; 32(3):275-282. PMC: 5606698. DOI: 10.1264/jsme2.ME17046. View

17.

Escudero C, Oggerin M, Amils R . The deep continental subsurface: the dark biosphere. Int Microbiol. 2019; 21(1-2):3-14. DOI: 10.1007/s10123-018-0009-y. View

18.

Yanagawa K, Tani A, Yamamoto N, Hachikubo A, Kano A, Matsumoto R . Biogeochemical Cycle of Methanol in Anoxic Deep-Sea Sediments. Microbes Environ. 2016; 31(2):190-3. PMC: 4912158. DOI: 10.1264/jsme2.ME15204. View

19.

Nishihara A, Matsuura K, Tank M, McGlynn S, Thiel V, Haruta S . Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs. Microbes Environ. 2018; 33(4):394-401. PMC: 6307999. DOI: 10.1264/jsme2.ME18041. View

20.

Tanaka Y, Tamaki H, Tanaka K, Tozawa E, Matsuzawa H, Toyama T . "Duckweed-Microbe Co-Cultivation Method" for Isolating a Wide Variety of Microbes Including Taxonomically Novel Microbes. Microbes Environ. 2018; 33(4):402-406. PMC: 6308005. DOI: 10.1264/jsme2.ME18067. View