in

Solutions in microbiome engineering: prioritizing barriers to organism establishment

  • 1.

    Inda ME, Broset E, Lu TK, de la Fuente-Nunez C. Emerging frontiers in microbiome engineering. Trends Immunol. 2019;40:952–73.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 2.

    Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Loffler FE, O’Malley MA, et al. Common principles and best practices for engineering microbiomes. Nat Rev Microbiol. 2019;17:725–41.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 3.

    Qiu ZG, Egidi E, Liu HW, Kaur S, Singh BK. New frontiers in agriculture productivity: optimised microbial inoculants and in situ microbiome engineering. Biotechnol Adv. 2019;37:107371.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 4.

    Enam F, Mansell TJ. Prebiotics: tools to manipulate the gut microbiome and metabolome. J Ind Microbiol Biotechnol. 2019;46:1445–59.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 5.

    Ke J, Wang B, Yoshikuni Y. Microbiome engineering: synthetic biology of plant-associated microbiomes in sustainable agriculture. Trends Biotechnol. 2021;39:244–61.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 6.

    Markowiak P, Slizewska K. Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients 2017;9:1021.

    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 7.

    Finkel OM, Castrillo G, Paredes SH, Gonzalez IS, Dangl JL. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol. 2017;38:155–63.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 8.

    Kaminsky LM, Trexler RV, Malik RJ, Hockett KL, Bell TH. The inherent conflicts in developing soil microbial inoculants. Trends Biotechnol. 2019;37:140–51.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 9.

    Kolar CS, Lodge DM. Progress in invasion biology: predicting invaders. Trends Ecol Evol. 2001;16:199–204.

    PubMed 
    Article 

    Google Scholar 

  • 10.

    Cairns J, Heckman JR. Restoration ecology: the state of an emerging field. Annu Rev Environ Resour. 1996;21:167–89.

    Google Scholar 

  • 11.

    Wainwright CE, Staples TL, Charles LS, Flanagan TC, Lai HR, Loy X, et al. Links between community ecology theory and ecological restoration are on the rise. J Appl Ecol. 2018;55:570–81.

    Article 

    Google Scholar 

  • 12.

    Mallon CA, Le Roux X, van Doorn GS, Dini-Andreote F, Poly F, Salles JF. The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche. ISME J. 2018;12:728–41.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 13.

    Enders M, Hutt MT, Jeschke JM. Drawing a map of invasion biology based on a network of hypotheses. Ecosphere. 2018;9:e02146.

    Article 

    Google Scholar 

  • 14.

    Catford JA, Jansson R, Nilsson C. Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework. Divers Distrib. 2009;15:22–40.

    Google Scholar 

  • 15.

    Wittmann MJ, Metzler D, Gabriel W, Jeschke JM. Decomposing propagule pressure: the effects of propagule size and propagule frequency on invasion success. Oikos 2014;123:441–50.

    Article 

    Google Scholar 

  • 16.

    Hulvey KB, Leger EA, Porensky LM, Roche LM, Veblen KE, Fund A, et al. Restoration islands: a tool for efficiently restoring dryland ecosystems? Restor Ecol. 2017;25:S124–S34.

    Article 

    Google Scholar 

  • 17.

    Funk JL, Hoffacker MK, Matzek V. Summer irrigation, grazing and seed addition differentially influence community composition in an invaded serpentine grassland. Restor Ecol. 2015;23:122–30.

    Article 

    Google Scholar 

  • 18.

    Jones ML, Ramoneda J, Rivett DW, Bell T. Biotic resistance shapes the influence of propagule pressure on invasion success in bacterial communities. Ecology 2017;98:1743–9.

    PubMed 
    Article 

    Google Scholar 

  • 19.

    Albright MBN, Sevanto S, Gallegos Graves LV, Dunbar J. Biotic interactions are more important than propagule pressure in microbial community invasions. Mbio 2020;11:e02089–20.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Vila JCC, Jones ML, Patel M, Bell T, Rosindell J. Uncovering the rules of microbial community invasions. Nat Ecol Evol. 2019;3:1162–71.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 21.

    Simberloff D. The role of propagule pressure in biological invasions. Annu Rev Ecol Evol Syst. 2009;40:81–102.

    Article 

    Google Scholar 

  • 22.

    Zhou JZ, Ning DL. Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol Rev. 2017;81:e00002–17.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 23.

    Comeau Y, Greer CW, Samson R. Role of inoculum preparation and density on the bioremediation of 2,4-D-contaminated soil by bioaugmentation. Appl Microbiol Biotechnol. 1993;38:681–7.

    Article 
    CAS 

    Google Scholar 

  • 24.

    Choudhary S, Schmidt-Dannert C. Applications of quorum sensing in biotechnology. Appl Microbiol Biotechnol. 2010;86:1267–79.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 25.

    Kreitschitz A, Haase E, Gorb SN. The role of mucilage envelope in the endozoochory of selected plant taxa. Sci Nat-Heidelb. 2021;108:2.

    Article 
    CAS 

    Google Scholar 

  • 26.

    Gornish E, Arnold H, Fehmi J. Review of seed pelletizing strategies for arid land restoration. Restor Ecol. 2019;27:1206–11.

    Article 

    Google Scholar 

  • 27.

    Ali M, Oshiki M, Rathnayake L, Ishii S, Satoh H, Okabe S. Rapid and successful start-up of anammox process by immobilizing the minimal quantity of biomass in PVA-SA gel beads. Water Res. 2015;79:147–57.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 28.

    Gallien L, Mazel F, Lavergne S, Renaud J, Douzet R, Thuiller W. Contrasting the effects of environment, dispersal and biotic interactions to explain the distribution of invasive plants in alpine communities. Biol Invasions. 2015;17:1407–23.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Cadotte MW, Campbell SE, Li SP, Sodhi DS, Mandrak NE. Preadaptation and naturalization of nonnative species: Darwin’s two fundamental insights into species invasion. Annu Rev Plant Biol. 2018;69:661–84.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 30.

    Fick SE, Day N, Duniway MC, Hoy-Skubik S, Barger NN. Microsite enhancements for soil stabilization and rapid biocrust colonization in degraded drylands. Restor Ecol. 2020;28:S139–S49.

    Article 

    Google Scholar 

  • 31.

    Vasquez E, Sheley R, Svejcar T. Creating invasion resistant soils via nitrogen management. Invas Plant Sci Man. 2008;1:304–14.

    Article 
    CAS 

    Google Scholar 

  • 32.

    Zhao X, Wang W, Blaine A, Kane ST, Zijlstra RT, Ganzle MG. Impact of probiotic Lactobacillus sp. on autochthonous lactobacilli in weaned piglets. J Appl Microbiol. 2019;126:242–54.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 33.

    Muthukrishnan R, Hansel-Welch N, Larkin DJ. Environmental filtering and competitive exclusion drive biodiversity-invasibility relationships in shallow lake plant communities. J Ecol. 2018;106:2058–70.

    Article 

    Google Scholar 

  • 34.

    Pereira FC, Berry D. Microbial nutrient niches in the gut. Environ Microbiol. 2017;19:1366–78.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 35.

    Thompson IP, van der Gast CJ, Ciric L, Singer AC. Bioaugmentation for bioremediation: the challenge of strain selection. Environ Microbiol. 2005;7:909–15.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 36.

    Bell TH, Bell T. Many roads to bacterial generalism. Fems Microbiol Ecol. 2021;97:fiaa240.

  • 37.

    Campieri M, Rizzello F, Venturi A, Poggioli G, Ugolini F, Helwig U, et al. Combination of antibiotic and probiotic treatment is efficacious in prophylaxis of post-operative recurrence of Crohn’s disease: a randomized controlled study vs mesalamine. Gastroenterology 2000;118:A781–A.

    Article 

    Google Scholar 

  • 38.

    Frese SA, Hutton AA, Contreras LN, Shaw CA, Palumbo MC, Casaburi G, et al. Persistence of supplemented Bifidobacterium longum subsp. infantis EVC001 in breastfed infants. Msphere. 2017;2:e00501–17.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Sasse J, Martinoia E, Northen T. Feed your friends: do plant exudates shape the root microbiome? Trends Plant Sci. 2018;23:25–41.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 40.

    Shepherd ES, DeLoache WC, Pruss KM, Whitaker WR, Sonnenburg JL. An exclusive metabolic niche enables strain engraftment in the gut microbiota. Nature 2018;557:434–8.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 41.

    Shaw AJ, Lam FH, Hamilton M, Consiglio A, MacEwen K, Brevnova EE, et al. Metabolic engineering of microbial competitive advantage for industrial fermentation processes. Science. 2016;353:583–6.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 42.

    Umu OCO, Rudi K, Diep DB. Modulation of the gut microbiota by prebiotic fibres and bacteriocins. Micro Ecol Health Dis. 2017;28:1348886.

    Google Scholar 

  • 43.

    Sriswasdi S, Yang CC, Iwasaki W. Generalist species drive microbial dispersion and evolution. Nat Commun. 2017;8:1162.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 44.

    McNally L, Brown SP. Building the microbiome in health and disease: niche construction and social conflict in bacteria. Philos Trans R Soc B. 2015;370:20140298.

    Article 

    Google Scholar 

  • 45.

    Shahab RL, Brethauer S, Luterbacher JS, Studer MH. Engineering of ecological niches to create stable artificial consortia for complex biotransformations. Curr Opin Biotechnol. 2020;62:129–36.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 46.

    Shade A, Peter H, Allison SD, Baho DL, Berga M, Burgmann H, et al. Fundamentals of microbial community resistance and resilience. Front Microbiol. 2012;3:417.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    Upton RN, Bach EM, Hofmockel KS. Spatio-temporal microbial community dynamics within soil aggregates. Soil Biol Biochem. 2019;132:58–68.

    Article 
    CAS 

    Google Scholar 

  • 48.

    Bezkorovainy A. Probiotics: determinants of survival and growth in the gut. Am J Clin Nutr. 2001;73:399s–405s.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 49.

    Tripathi S, Srivastava P, Devi R, Bhadouria R. Influence of synthetic fertilizers and pesticides on soil health and soil microbiology. In: Prasad MNV (ed). Agrochemicals detection, treatment and remediation. (Butterworth-Heinemann, 2020) pp 25-54.

  • 50.

    Dykhuizen DE, Hartl DL. Selection in chemostats. Microbiol Rev. 1983;47:150–68.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 51.

    Zhao D, Wu SG, Feng WW, Jakovlic I, Tran NT, Xiong F. Adhesion and colonization properties of potentially probiotic Bacillus paralicheniformis strain FA6 isolated from grass carp intestine. Fish Sci. 2020;86:153–61.

    Article 
    CAS 

    Google Scholar 

  • 52.

    Wang XY, Cao ZP, Zhang MM, Meng L, Ming ZZ, Liu JY. Bioinspired oral delivery of gut microbiota by self-coating with biofilms. Sci Adv. 2020;6:eabb1952.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 53.

    Ali SA, Singh P, Tomar SK, Mohanty AK, Behare P. Proteomics fingerprints of systemic mechanisms of adaptation to bile in Lactobacillus fermentum. J Proteom. 2020;213:103600.

    Article 
    CAS 

    Google Scholar 

  • 54.

    Wisz MS, Pottier J, Kissling WD, Pellissier L, Lenoir J, Damgaard CF, et al. The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling. Biol Rev. 2013;88:15–30.

    PubMed 
    Article 

    Google Scholar 

  • 55.

    Funk JL, Cleland EE, Suding KN, Zavaleta ES. Restoration through reassembly: plant traits and invasion resistance. Trends Ecol Evol. 2008;23:695–703.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 56.

    Northfield TD, Laurance SGW, Mayfield MM, Paini DR, Snyder WE, Stouffer DB, et al. Native turncoats and indirect facilitation of species invasions. Proc Biol Sci. 2018;285:20171936.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 57.

    Gagnon K, Rinde E, Bengil EGT, Carugati L, Christianen MJA, Danovaro R, et al. Facilitating foundation species: the potential for plant-bivalve interactions to improve habitat restoration success. J Appl Ecol. 2020;57:1161–79.

    Article 

    Google Scholar 

  • 58.

    Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell 2018;174:1406–23.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 59.

    Garcia-Bayona L, Comstock LE. Bacterial antagonism in host-associated microbial communities. Science. 2018;361:eaat2456.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 60.

    Maynard DS, Crowther TW, Bradford MA. Competitive network determines the direction of the diversity-function relationship. Proc Natl Acad Sci USA. 2017;114:11464–9.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 61.

    Feichtmayer J, Deng L, Griebler C. Antagonistic microbial interactions: contributions and potential applications for controlling pathogens in the aquatic systems. Front Microbiol. 2017;8:2192.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 62.

    Fuchslin HP, Schneider C, Egli T. In glucose-limited continuous culture the minimum substrate concentration for growth, s(min), is crucial in the competition between the enterobacterium Escherichia coli and Chelatobacter heintzii, an environmentally abundant bacterium. ISME J. 2012;6:777–89.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 63.

    Beaury EM, Finn JT, Corbin JD, Barr V, Bradley BA. Biotic resistance to invasion is ubiquitous across ecosystems of the United States. Ecol Lett. 2020;23:476–82.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 64.

    Eisenhauer N, Schulz W, Scheu S, Jousset A. Niche dimensionality links biodiversity and invasibility of microbial communities. Funct Ecol. 2013;27:282–8.

    Article 

    Google Scholar 

  • 65.

    Panigrahi P, Parida S, Nanda NC, Satpathy R, Pradhan L, Chandel DS, et al. A randomized synbiotic trial to prevent sepsis among infants in rural India. Nature. 2017;548:407–12.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 66.

    Perez-Gutierrez RA, Lopez-Ramirez V, Islas A, Alcaraz LD, Hernandez-Gonzalez I, Olivera BCL, et al. Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network. ISME J. 2013;7:487–97.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 67.

    Safferman RS, Morris ME. Evaluation of natural products for algicidal properties. Appl Microbiol. 1962;10:289–92.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 68.

    Russel J, Roder HL, Madsen JS, Burmolle M, Sorensen SJ. Antagonism correlates with metabolic similarity in diverse bacteria. Proc Natl Acad Sci USA. 2017;114:10684–8.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 69.

    Long RA, Rowley DC, Zamora E, Liu JY, Bartlett DH, Azam F. Antagonistic interactions among marine bacteria impede the proliferation of Vibrio cholerae. Appl Environ Microbiol. 2005;71:8531–6.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 70.

    Hecht AL, Casterline BW, Earley ZM, Goo YA, Goodlett DR, Wardenburg JB. Strain competition restricts colonization of an enteric pathogen and prevents colitis. EMBO Rep. 2016;17:1281–91.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 71.

    Lopez-Igual R, Bernal-Bayard J, Rodriguez-Paton A, Ghigo JM, Mazel D. Engineered toxin-intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations. Nat Biotechnol. 2019;37:755–60.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 72.

    Koskella B. New approaches to characterizing bacteria-phage interactions in microbial communities and microbiomes. Environ Microbiol Rep. 2019;11:15–6.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 73.

    Soundararajan M, von Bunau R, Oelschlaeger TA. K5 Capsule and lipopolysaccharide are important in resistance to T4 phage attack in probiotic E. coli strain nissle 1917. Front Microbiol. 2019;10:2783.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 74.

    Thingstad TF. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr. 2000;45:1320–8.

    Article 

    Google Scholar 

  • 75.

    Marsh P, Wellington EMH. Phage-host interactions in soil. FEMS Microbiol Ecol. 1994;15:99–107.

    Article 
    CAS 

    Google Scholar 

  • 76.

    Balogh B, Jones JB, Iriarte FB, Momol MT. Phage therapy for plant disease control. Curr Pharm Biotechnol. 2010;11:48–57.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 77.

    Foster KR, Bell T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr Biol. 2012;22:1845–50.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 78.

    Piccardi P, Vessman B, Mitri S. Toxicity drives facilitation between 4 bacterial species. Proc Natl Acad Sci USA. 2019;116:15979–84.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 79.

    Pascual-Garcia A, Bonhoeffer S, Bell T. Metabolically cohesive microbial consortia and ecosystem functioning. Philos Trans R Soc B. 2020;375:20190245.

    Article 
    CAS 

    Google Scholar 

  • 80.

    Martinez-Harms MJ, Bryan BA, Balvanera P, Law EA, Rhodes JR, Possingham HP, et al. Making decisions for managing ecosystem services. Biol Conserv. 2015;184:229–38.

    Article 

    Google Scholar 

  • 81.

    Kildisheva OA, Dixon KW, Silveira FAO, Chapman T, Di Sacco A, Mondoni A, et al. Dormancy and germination: making every seed count in restoration. Restor Ecol. 2020;28:S256–S65.

    Article 

    Google Scholar 

  • 82.

    Maslo B, Handel SN, Pover T. Restoring beaches for Atlantic coast piping plovers (Charadrius melodus): a classification and regression tree analysis of nest-site selection. Restor Ecol. 2011;19:194–203.

    Article 

    Google Scholar 

  • 83.

    Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10:538–50.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 84.

    Carr A, Diener C, Baliga NS, Gibbons SM. Use and abuse of correlation analyses in microbial ecology. ISME J. 2019;13:2647–55.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 85.

    Estes JA, Terborgh J, Brashares JS, Power ME, Berger J, Bond WJ, et al. Trophic downgrading of planet Earth. Science. 2011;333:301–6.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 86.

    Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol. 2014;5:219.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 87.

    Herren CM, McMahon KD. Keystone taxa predict compositional change in microbial communities. Environ Microbiol. 2018;20:2207–17.

    PubMed 
    Article 

    Google Scholar 

  • 88.

    Trosvik P, de Muinck EJ. Ecology of bacteria in the human gastrointestinal tract-identification of keystone and foundation taxa. Microbiome. 2015;3:44.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 89.

    Kopp-Hoolihan L. Prophylactic and therapeutic uses of probiotics: a review. J Am Diet Assoc. 2001;101:229–41.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 90.

    Woo SL, Pepe O. Microbial consortia: promising probiotics as plant biostimulants for sustainable agriculture. Front Plant Sci. 2018;9:1801.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 91.

    Wood-Charlson EM, Anubhav, Auberry D, Blanco H, Borkum MI, Corilo YE, et al. The National Microbiome Data Collaborative: enabling microbiome science. Nat Rev Microbiol. 2020;18:313–4.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 92.

    Brussow H. Probiotics and prebiotics in clinical tests: an update. F1000Res. 2019;8:1157.

  • 93.

    van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368:407–15.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 94.

    Weingarden AR, Chen C, Bobr A, Yao D, Lu YW, Nelson VM, et al. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am J Physiol Gastrointest Liver Physiol. 2014;306:G310–G9.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 95.

    Hutchinson MI, Bell TAS, Gallegos-Graves L, Dunbar J, Albright M. Merging fungal and bacterial community profiles via an internal control. Microb Ecol. 2021; e-pub ahead of print 2021; https://doi.org/10.1007/s00248-020-01638-y.

  • 96.

    Nayfach S, Roux S, Seshadri R. A genomic catalog of Earth’s micobiomes. Nat Biotechnol. 2021;39:499–509. al. e

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 97.

    Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3:160018.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 98.

    Azubuike CC, Chikere CB, Okpokwasili GC. Bioremediation techniques-classification based on site of application: principles, advantages, limitations and prospects. World J Microbiol Biotechnol. 2016;32:180.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 99.

    Henze M, Gujer W, Mino T, Van Loosdrecht MCM. Activated sludge models ASM1, ASM2, ASM2d and ASM, Vol 121. 2000. IWA Scientific and Technical Report 9, IWA publishing, London.

  • 100.

    Orozco-Mosqueda MD, Rocha-Granados MD, Glick BR, Santoyo G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res. 2018;208:25–31.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 


  • Source: Ecology - nature.com

    Description of larval morphology and phylogenetic relationships of Heterotemna tenuicornis (Silphidae)

    Countering climate change with cool pavements