Book contents
- Microbiomes of Soils, Plants and Animals
- Ecological Reviews
- Microbiomes of Soils, Plants and Animals
- Copyright page
- Contents
- Contributors
- Preface
- Abbreviations
- Chapter One Microbiomes of soils, plants and animals: an introduction
- Chapter Two Analytical approaches for microbiome research
- Chapter Three Microbiomes of soils
- Chapter Four Factors that shape the host microbiome
- Chapter Five Microbial symbioses and host nutrition
- Chapter Six The microbiome and host behaviour
- Chapter Seven Host microbiomes and disease
- Chapter Eight Adapting to environmental change
- Chapter Nine Microbial biotechnology
- Chapter Ten Synthesis and future directions
- Index
- Plate Section (PDF Only)
- References
Chapter Nine - Microbial biotechnology
Published online by Cambridge University Press: 07 March 2020
Book contents
- Microbiomes of Soils, Plants and Animals
- Ecological Reviews
- Microbiomes of Soils, Plants and Animals
- Copyright page
- Contents
- Contributors
- Preface
- Abbreviations
- Chapter One Microbiomes of soils, plants and animals: an introduction
- Chapter Two Analytical approaches for microbiome research
- Chapter Three Microbiomes of soils
- Chapter Four Factors that shape the host microbiome
- Chapter Five Microbial symbioses and host nutrition
- Chapter Six The microbiome and host behaviour
- Chapter Seven Host microbiomes and disease
- Chapter Eight Adapting to environmental change
- Chapter Nine Microbial biotechnology
- Chapter Ten Synthesis and future directions
- Index
- Plate Section (PDF Only)
- References
Summary
Microbes provide a diverse source of functional traits that can be used to address a whole range of human and environmental problems, from agriculture and farming, to human and wildlife health, and energy production and climate change mitigation. Although microbes and their derivatives have been used for decades in some contexts, recent advances in sequencing and other technologies have allowed us to identify and understand novel sources and applications. Here, we review a range of different types of microbial biotechnology, including probiotics or microbial inputs, prebiotics, enzybiotics, microbiome transplants, antimicrobial peptides and secondary metabolites, across a range of contexts including human health, agriculture, biofuel production and wildlife disease, among others. We discuss the advances made in these fields, along with the complexities and problems associated with success. We also comment on ethical issues surrounding the use of microbial biotechnology and areas of policy and risk assessment that will need to develop to promote safe implementation.
Keywords
- Type
- Chapter
- Information
- Microbiomes of Soils, Plants and AnimalsAn Integrated Approach, pp. 182 - 221Publisher: Cambridge University PressPrint publication year: 2020
References
Adam, E, Groenenboom, AE, Kurm, V, et al. (2016) Controlling the microbiome: Microhabitat adjustments for successful biocontrol strategies in soil and human gut. Frontiers in Microbiology, 7, 1079.Google Scholar
Adame-Álvarez, RM, Mendiola-Soto, J, Heil, M. (2014) Order of arrival shifts endophyte–pathogen interactions in bean from resistance induction to disease facilitation. FEMS Microbiology Letters, 355, 100–107.Google Scholar
Adesemoye, AO, Torbert, HA, Kloepper, JW. (2009) Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Microbial Ecology, 58, 921–929.Google Scholar
Allen, HK, Levine, UY, Looft, T, et al. (2013) Treatment, promotion, commotion: Antibiotic alternatives in food-producing animals. Trends in Microbiology, 21, 114–119.Google Scholar
Allgaier, M, Reddy, A, Park, J, et al. (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS ONE, 5, e8812.CrossRefGoogle ScholarPubMed
Alves, LdF, Westmann, CA, Lovate, GL, et al. (2018) Metagenomic approaches for understanding new concepts in microbial science. International Journal of Genomics, 2018, 2312987.CrossRefGoogle ScholarPubMed
Amoutzias, GD, Chaliotis, A, Mossialos, D. (2016) Discovery strategies of bioactive compounds synthesized by nonribosomal peptide synthetases and type-I polyketide synthases derived from marine microbiomes. Marine Drugs, 14, 80.Google Scholar
Antwis, RE, Preziosi, RF, Harrison, XA, et al. (2015) Amphibian symbiotic bacteria do not show a universal ability to inhibit growth of the global panzootic lineage of Batrachochytrium dendrobatidis. Applied and Environmental Microbiology, 81, 3706–3711.Google Scholar
Antwis, RE, Harrison, XA. (2018) Probiotic consortia are not uniformly effective against different amphibian chytrid pathogen isolates. Molecular Ecology, 27, 577–589.Google Scholar
Antwis, RE, Griffiths, SM, Harrison, XA, et al. (2017) Fifty important research questions in microbial ecology. FEMS Microbiology Ecology, 93, fix044.CrossRefGoogle ScholarPubMed
Arraktham, S, Tancho, A, Niamsup, P, et al. (2016) The potential of bacteria isolated from earthworm intestines, vermicompost and liquid vermicompost to produce indole-3-acetic acid (IAA). Journal of Agricultural Technology, 12, 229–239.Google Scholar
Atterbury, RJ, Hobley, L, Till, R, et al. (2011) Effects of orally administered Bdellovibrio bacteriovorus on the well-being and Salmonella colonization of young chicks. Applied and Environmental Microbiology, 77, 5794–5803.CrossRefGoogle ScholarPubMed
Bakken, JS, Borody, T, Brandt, LJ, et al. (2011) Treating Clostridium difficile infection with fecal microbiota transplantation. Clinical Gastroenterology and Hepatology, 9, 1044–1049.Google Scholar
Batista‐García, RA, del Rayo Sánchez‐Carbente, M, Talia, P, et al. (2016) From lignocellulosic metagenomes to lignocellulolytic genes: Trends, challenges and future prospects. Biofuels, Bioproducts and Biorefining, 10, 864–882.Google Scholar
Becker, MH, Walke, JB, Murrill, L, et al. (2015) Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis. Molecular Ecology, 24, 1628–1641.Google Scholar
Bender, SF, Wagg, C, van der Heijden, MGA. (2016) An underground revolution: Biodiversity and soil ecological engineering for agricultural sustainability. Trends in Ecology & Evolution, 31, 440–452.Google Scholar
Bender, SF, Wagg, C, van der Heijden, MGA. (2017) Strategies for environmentally sound soil ecological engineering: A reply to Machado et al. Trends in Ecology & Evolution, 32, 10–12.Google Scholar
Berruti, A, Lumini, E, Balestrini, R, et al. (2016) Arbuscular mycorrhizal fungi as natural biofertilizers: Let’s benefit from past successes. Frontiers in Microbiology, 6, 1–13.Google Scholar
Bhardwaj, D, Ansari, MW, Sahoo, RK, et al. (2014) Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity. Microbial Cell Factories, 13, 1–10.Google Scholar
Blajman, J, Gaziano, C, Zbrun, MV, et al. (2015) In vitro and in vivo screening of native lactic acid bacteria toward their selection as a probiotic in broiler chickens. Research in Veterinary Science, 101, 50–56.Google Scholar
Bletz, MC, Loudon, AH, Becker, MH, et al. (2013) Mitigating amphibian chytridiomycosis with bioaugmentation: Characteristics of effective probiotics and strategies for their selection and use. Ecology Letters, 16, 807–20.CrossRefGoogle ScholarPubMed
Bletz, MC, Myers, J, Woodhams, DC, et al. (2017) Estimating herd immunity to amphibian chytridiomycosis in Madagascar based on the defensive function of amphibian skin bacteria. Frontiers in Microbiology, 8, 1751.Google Scholar
Blumenstein, K, Albrectsen, BR, Martín, JA, et al. (2015) Nutritional niche overlap potentiates the use of endophytes in biocontrol of a tree disease. BioControl, 60, 655–667.Google Scholar
Bowles, TM, Jackson, LE, Loeher, M, et al. (2017) Ecological intensification and arbuscular mycorrhizas: A meta-analysis of tillage and cover crop effects. Journal of Applied Ecology, 54, 1785–1793.Google Scholar
Boyle, RJ, Bath-Hextall, FJ, Leonardi-Bee, J, et al. (2009) Probiotics for the treatment of eczema: Asystematic review. Clinical and Experimental Allergy, 39, 1117–1127.Google Scholar
Brennan, EB, Acosta-Martinez, V. (2017) Cover cropping frequency is the main driver of soil microbial changes during six years of organic vegetable production. Soil Biology and Biochemistry, 109, 188–204.Google Scholar
Brennan, Y, Callen, WN, Christoffersen, L, et al. (2004) Unusual microbial xylanases from insect guts. Applied and Environmental Microbiology, 70, 3609–3617.Google Scholar
Briers, Y, Walmagh, M, Van Puyenbroeck, V, et al. (2015) Engineered endolysin-based ‘artilysins’ to combat multidrug-resistant Gram-negative pathogens. mBio, 5, e01379–14.Google Scholar
Brown, P, Saa, S. (2015) Biostimulants in agriculture. Frontiers in Plant Science, 6, 671.Google Scholar
Busby, PE, Soman, C, Wagner, MR, et al. (2017) Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biology, 15, 1–14.Google Scholar
Calderón-Cortés, N, Quesada, M, Watanabe, H, et al. (2012) Endogenous plant cell wall digestion: A key mechanism in insect evolution. Annual Review of Ecology, Evolution, and Systematics, 43, 45–71.Google Scholar
Calvo, P, Nelson, L, Kloepper, JW. (2014) Agricultural uses of plant biostimulants. Plants and Soil, 383, 3–41.Google Scholar
Cardoso, AM, Cavalcante, JJ, Cantão, ME, et al. (2012a) Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes. PLoS ONE, 7, e48505.Google Scholar
Cardoso, AM, Cavalcante, JJV, Vieira, RP, et al. (2012b) Gut bacterial communities in the giant landsnail Achatina fulica and their modification by a sugarcane-based diet. PLoS ONE, 7, e33440.Google Scholar
Carro, L, Nouioui, I. (2017) Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiology, 3, 383–412.Google Scholar
Cavaglieri, LR, Passone, A, Etcheverry, MG. (2004) Correlation between screening procedures to select root endophytes for biological control of Fusarium verticillioides in Zea mays L. Biological Control, 31, 259–267.Google Scholar
Chagnot, C, Zorgani, MA, Astruc, T, et al. (2013) Proteinaceous determinants of surface colonization in bacteria: Bacterial adhesion and biofilm formation from a protein secretion perspective. Frontiers in Microbiology, 4, 1–26.Google Scholar
Chaparro, JM, Badri, DV, Bakker, MG, et al. (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS ONE, 8, e55731.CrossRefGoogle ScholarPubMed
Chaudhry, V, Rehman, A, Mishra, A, et al. (2012) Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microbial Ecology, 64, 450–460.Google Scholar
Cisek, AA, Dąbrowska, I, Gregorczyk, KP, et al. (2017) Phage therapy in bacterial infections treatment: One hundred years after the discovery of bacteriophages. Current Microbiology, 74, 277–283.Google Scholar
Colás Sánchez, A, Torres Gutiérrez, R, Cupull Santana, R, et al. (2014) Effects of co-inoculation of native Rhizobium and Pseudomonas strains on growth parameters and yield of two contrasting Phaseolus vulgaris L. genotypes under Cuban soil conditions. European Journal of Soil Biology, 62, 105–112.CrossRefGoogle Scholar
Colombo, BM, Scalvenzi, T, Benlamara, S, et al. (2015) Microbiota and mucosal immunity in amphibians. Frontiers in Immunology, 6, 111.CrossRefGoogle ScholarPubMed
Cottrell, MT, Moore, JA, Kirchman, DL. (1999) Chitinases from uncultured marine microorganisms. Applied and Environmental Microbiology, 65, 2553–2557.Google Scholar
Crist, E, Mora, C, Engelman, R. (2017) The interaction of human population, food production, and biodiversity protection. Science, 264, 260–264.CrossRefGoogle Scholar
Cuello-Garcia, C.A, Brozek, JL, Fiocchi, A, et al. (2015) Probiotics for the prevention of allergy: A systematic review and meta-analysis of randomized controlled trials. Journal of Allergy and Clinical Immunology, 136, 952–961.CrossRefGoogle ScholarPubMed
Dale, C, Moran, NA. (2006) Molecular interactions between bacterial symbionts and their hosts. Cell, 126, 453–465.Google Scholar
Daniel, C, Sebbane, F, Poiret, S, et al. (2009) Protection against Yersinia pseudotuberculosis infection conferred by a Lactococcus lactis mucosal delivery vector secreting LcrV. Vaccine, 27, 1141–1144.CrossRefGoogle ScholarPubMed
Dar, MA, Pawar, KD, Pandit, RS. (2017) Gut microbiome analysis of snails: A biotechnological approach. In: Ray, S (Ed.) Organismal and Molecular Malacology. London: InTech Open.Google Scholar
Daskin, JH, Alford, RA. (2012) Context-dependent symbioses and their potential roles in wildlife diseases. Proceedings of the Royal Society B: Biological Sciences, 279, 1457–1465.CrossRefGoogle ScholarPubMed
Daskin, JH, Bell, SC, Schwarzkopf, L, et al. (2014) Cool temperatures reduce antifungal activity of symbiotic bacteria of threatened amphibians – Implications for disease management and patterns of decline. PLoS ONE, 9, e100378.CrossRefGoogle ScholarPubMed
Davidson, DH. (1976) Assimilation efficiencies of slugs on different food materials. Oecologia, 26, 267–273.Google Scholar
De Boer, W, Wagenaar, AM, Klein Gunnewiek, PJA, et al. (2007) In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria. FEMS Microbiology Ecology, 59, 177–185.Google Scholar
De La Fuente, L, Mavrodi, DV, Landa, BB, et al. (2006) phlD-based genetic diversity and detection of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens. FEMS Microbiology Ecology, 56, 64–78.Google Scholar
De Nobili, M, Contin, M, Mondini, C, et al. (2001) Soil microbial biomass is triggered into activity by trace amounts of substrate. Biology and Fertility of Soils, 33, 1163–1170.Google Scholar
De Roy, K, Marzorati, M, Van den Abbeele, P, et al. (2014) Synthetic microbial ecosystems: An exciting tool to understand and apply microbial communities. Environmental Microbiology, 16, 1472–1481.CrossRefGoogle ScholarPubMed
Denev, S, Chevaux, E, Demey, ECV. (2013) Efficacite du probiotique Pediococcus acidilactici sur les performances zootechniques de poules pondeuses. Dixièmes Journées de la Recherche Avicole et Palmipèdes à Foie Gras, 2013, 943–946.Google Scholar
Denou, E, Pridmore, RD, Berger, B, et al. (2008) Identification of genes associated with the long-gut-persistence phenotype of the probiotic Lactobacillus johnsonii strain NCC533 using a combination of genomics and transcriptome analysis. Journal of Bacteriology, 190, 3161–3168.Google Scholar
Derua, YA, Kahindi, SC, Mosha, FW, et al. (2018) Microbial larvicides for mosquito control: Impact of long lasting formulations of Bacillus thuringiensis var. israelensis and Bacillus sphaericus on non-target organisms in western Kenya highlands. Ecology and Evolution, 8, 7563–7573.CrossRefGoogle ScholarPubMed
Di Benedetto, AN, Rosaria Corbo, M, Campaniello, D, et al. (2017) The role of plant growth promoting bacteria in improving nitrogen use efficiency for sustainable crop production: A focus on wheat. AIMS Microbiology, 3, 413–434.CrossRefGoogle Scholar
Donohoue, PD, Barrangou, R, May, AP. (2018) Advances in industrial biotechnology using CRISPR-Cas systems. Trends in Biotechnology, 36, 134–146.Google Scholar
Douglas, AE. (2013) Microbial brokers of insect-plant interactions revisited. Journal of Chemical Ecology, 39, 952–961.Google Scholar
Draper, K, Ley, C, Parsonnet, J. (2017) Probiotic guidelines and physician practice: A cross-sectional survey and overview of the literature. Beneficial Microbes, 8, 507–519.CrossRefGoogle Scholar
Dwivedi, SL, Van Bueren, ETL, Ceccarelli, S, et al. (2017) Diversifying food systems in the pursuit of sustainable food production and healthy diets. Trends in Plant Science, 22, 842–856.Google Scholar
Eisenhauer, N, Scheu, S, Jousset, A. (2012) Bacterial diversity stabilizes community productivity. PLoS ONE, 7, e34517.Google Scholar
Eisenhauer, N, Schulz, W, Scheu, S, et al. (2013) Niche dimensionality links biodiversity and invasibility of microbial communities. Functional Ecology, 27, 282–8.Google Scholar
El Khoury, S, Rousseau, A, Lecoeur, A, et al. (2018) Deleterious interaction between honeybees (Apis mellifera) and its microsporidian intracellular parasite Nosema ceranae was mitigated by administrating either endogenous or allochthonous gut microbiota strains. Frontiers in Ecology and Evolution, 6, 58.Google Scholar
Elend, C, Schmeisser, C, Leggewie, C, et al. (2006) Isolation and biochemical characterization of two novel metagenome-derived esterases. Applied and Environmental Microbiology, 72, 3637–3645.CrossRefGoogle ScholarPubMed
Emam, T. (2016) Local soil, but not commercial AMF inoculum, increases native and non‐native grass growth at a mine restoration site. Restoration Ecology, 24, 35–44.CrossRefGoogle Scholar
Evans, JD, Lopez, DL. (2004) Bacterial probiotics induce an immune response in the honey bee (Hymenoptera: Apidae). Journal of Economic Entomology, 97, 752–756.CrossRefGoogle ScholarPubMed
Feng, YD, Duan, CJ, Pang, H, et al. (2007) Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases. Applied Microbiology and Biotechnology, 75, 319–328.Google Scholar
Ferrer, M, Golyshina, OV, Chernikova, TN, et al. (2005) Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environmental Microbiology, 7, 1966–2010.Google Scholar
Ferrer, M, Martínez-Martínez, M, Bargiela, R, et al. (2016) Estimating the success of enzyme bioprospecting through metagenomics: Current status and future trends. Microbial Biotechnology, 9, 22–34.Google Scholar
Finkel, OM, Castrillo, G, Herrera Paredes, S, et al. (2017) Understanding and exploiting plant beneficial microbes. Current Opinion in Plant Biology, 38, 155–163.Google Scholar
Fischetti, VA. (2010) Bacteriophage endolysins: A novel anti-infective to control Gram-positive pathogens. International Journal of Medical Microbiology, 300, 357–362.Google Scholar
Flohre, A, Rudnick, M, Traser, G, et al. (2011) Does soil biota benefit from organic farming in complex vs. simple landscapes? Agriculture, Ecosystems and Environment, 141, 210–214.Google Scholar
Flores, HA, O’Neill, SL. (2018) Controlling vector-borne diseases by releasing modified mosquitoes. Nature Reviews Microbiology, 16, 508–518.Google Scholar
Foo, JL, Ling, H, Lee, YS, et al. (2017) Microbiome engineering: Current applications and its future. Biotechnology Journal, 12, 1–11.Google Scholar
Ford, SA, Kao, D, Williams, D, et al. (2016) Microbe-mediated host defence drives the evolution of reduced pathogen virulence. Nature Communications, 7, 13430.CrossRefGoogle ScholarPubMed
Forey, E, Chauvat, M, Coulibaly, SFM, et al. (2018) Inoculation of an ecosystem engineer (Earthworm: Lumbricus terrestris) during experimental grassland restoration: Consequences for above and belowground soil compartments. Applied Soil Ecology, 125, 148–155.Google Scholar
Gagliardi, A, Totino, V, Cacciotti, F, et al. (2018) Rebuilding the gut microbiota ecosystem. International Journal of Environmental Research and Public Health, 15, 1679.Google Scholar
García-Cayuela, T, Requena, T, Martínez-Cuesta, MC, et al. (2017) Rapid detection of Lactococcus lactis isolates producing the lantibiotics nisin, lacticin 481 and lacticin 3147 using MALDI-TOF MS. Journal of Microbiology Methods, 139, 138–142.Google Scholar
Genta, FA, Dillon, RJ, Terra, WR, et al. (2006) Potential role for gut microbiota in cell wall digestion and glucoside detoxification in Tenebrio molitor larvae. Journal of Insect Physiology, 52, 593–601.Google Scholar
Glanville, J, King, S, Guarner, F, et al. (2015) A review of the systematic review process and its applicability for use in evaluating evidence for health claims on probiotic foods in the European Union. Nutrition Journal, 14, 16.CrossRefGoogle ScholarPubMed
Gram, L, Løvold, T, Nielsen, J, et al. (2001) In vitro antagonism of the probiont Pseudomonas fluorescens strain AH2 against Aeromonas salmonicida does not confer protection of salmon against furunculosis. Aquaculture, 199, 1–11.Google Scholar
Grant, S, Sorokin, DY, Grant, WD, et al. (2004) A phylogenetic analysis of Wadi el Natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures. Extremophiles, 8, 421–429.Google Scholar
Gutleben, J, Chaib De Mares, M, van Elsas, JD, et al. (2018) The multi-omics promise in context: From sequence to microbial isolate. Critical Reviews in Microbiology, 44, 212–229.Google Scholar
Hamilton, JJ, Garcia, SL, Brown, BS, et al. (2017) Metabolic network analysis and metatranscriptomics reveal auxotrophies and nutrient sources of the cosmopolitan freshwater microbial lineage acI. mSystems, 2, 1–13.Google Scholar
Hancock, REW, Haney, EF, Gill, EE. (2016) The immunology of host defence peptides: Beyond antimicrobial activity. Nature Reviews Immunology, 16, 321–334.Google Scholar
Hansen, AK, Moran, NA. (2014) The impact of microbial symbionts on host plant utilization by herbivorous insects. Molecular Ecology, 23, 1473–1496.Google Scholar
Hartmann, M, Frey, B, Mayer, J, et al. (2015) Distinct soil microbial diversity under long-term organic and conventional farming. The ISME Journal, 9, 1177–1194.Google Scholar
Hempel, S, Newberry, SJ, Maher, AR, et al. (2012) Probiotics for the prevention and treatment of antibiotic-associated diarrhea. JAMA, 307, 1959–1969.Google Scholar
Hernández, M, Chailloux, M. (2004) Las micorrizas arbusculares y las bacterias rizosféricas como alternativa a la nutrición mineral del tomate. Cultivos Tropicales, 25, 5–12.Google Scholar
Hess, M, Sczyrba, A, Egan, R, et al. (2011) Metagenomic sequencing of biomass-degrading microbes from cow rumen reveals new carbohydrate-active enzymes. Science, 28, 463–467.Google Scholar
HM Government. (2019) Contained and controlled: The UK’s 20-year vision for antimicrobial resistance. Available at: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/773065/uk-20-year-vision-for-antimicrobial-resistance.pdfGoogle Scholar
Hojckova, K, Stano, M, Klucar, L. (2013) PhiBIOTICS: Catalogue of therapeutic enzybiotics, relevant research studies and practical applications. BMC Microbiology, 13, 53.Google Scholar
Holden, WM, Hanlon, SM, Woodhams, DC, et al. (2015) Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis. Biological Conservation, 187, 91–102.Google Scholar
Hong, HA, Le, HD, Cutting, SM. (2005) The use of bacterial spore formers as probiotics. FEMS Microbiology Reviews, 29, 813–835.Google Scholar
Hoyt, JR, Cheng, TL, Langwig, KE, et al. (2015) Bacteria isolated from bats inhibit the growth of Pseudogymnoascus destructans, the causative agent of white-nose syndrome. PLoS ONE, 10, e0121329.Google Scholar
Hu, J, Wei, Z, Friman, VP, et al. (2016) Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression. mBio, 7, 1–8.Google Scholar
Hu, J, Wei, Z, Weidner, S, et al. (2017) Probiotic Pseudomonas communities enhance plant growth and nutrient assimilation via diversity-mediated ecosystem functioning. Soil Biology and Biochemistry, 113, 122–129.Google Scholar
Hulston, CJ, Chrunside, AA, Venables, MC. (2015) Probiotic supplementation prevents high-fat, overfeeding-induced insulin resistance in human subjects. British Journal of Nutrition, 113, 595–602.CrossRefGoogle ScholarPubMed
Hussain, N, Singh, A, Saha, S, et al. (2016) Excellent N-fixing and P-solubilizing traits in earthworm gut-isolated bacteria: A vermicompost based assessment with vegetable market waste and rice straw feed mixtures. Bioresource Technology, 222, 165–174.Google Scholar
Huws, SA, Creevey, CJ, Oyama, LB, et al. (2018) Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future. Frontiers in Microbiology, 9, 2161.Google Scholar
Ianiro, G, Valerio, L, Mascucci, L, et al. (2017) Predictors of failure after single faecal microbiota transplantation in patients with recurrent Clostridium difficile infection: Results from a 3-year, single-centre cohort study. Clinical Microbiology and Infection, 23, 337.Google Scholar
Imperiali, N, Dennert, F, Schneider, J, et al. (2017) Relationships between root pathogen resistance, abundance and expression of Pseudomonas antimicrobial genes, and soil properties in representative Swiss agricultural soils. Frontiers in Plant Science, 8, 1–22.CrossRefGoogle ScholarPubMed
Ishaq, SL, Johnson, SP, Miller, ZJ, et al. (2017) Impact of cropping systems, soil inoculum, and plant species identity on soil bacterial community structure. Microbial Ecology, 73, 417–434.CrossRefGoogle ScholarPubMed
James, CE. (2013) Recent advances in studies of polymicrobial interactions in oral biofilms. Current Oral Health Reports, 1, 59–69.Google Scholar
Jani, AJ, Briggs, CJ. (2014) The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection. Proceedings of the National Academy of Sciences, 111, E5049–5058.Google Scholar
Jiménez, RR, Sommer, S. (2017) The amphibian microbiome: Natural range of variation, pathogenic dysbiosis, and role in conservation. Biodiversity and Conservation, 26, 763–786.Google Scholar
Jones, SE, Lennon, JT. (2010) Dormancy contributes to the maintenance of microbial diversity. Proceedings of the National Academy of Sciences, 107, 5881–5886.Google Scholar
Jousset, A, Schulz, W, Scheu, S, et al. (2011) Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. The ISME Journal, 5, 1108–1114.Google Scholar
Jousset, A, Becker, J, Chatterjee, S, et al. (2014) Biodiversity and species identity shape the antifungal activity of bacterial communities. Ecology, 95, 1184–1190.Google Scholar
Joynson, R, Pritchard, L, Osemwekha, E, et al. (2017) Metagenomic analysis of the gut microbiome of the common black slug Arion ater in search of novel lignocellulose degrading enzymes. Frontiers in Microbiology, 8, 2181.Google Scholar
Kaminsky, LM, Trexler, RV, Malik, RJ, et al. (2018). The inherent conflicts in developing soil microbial inoculants. Trends in Biotechnology, 37, 140–151.Google Scholar
Kaznowski, A, Szymas, B, Jazdzinska, E, et al. (2004) The effects of probiotic supplementation on the content of intestinal microflora and chemical composition of worker honey bees (Apis mellifera). Journal of Apicultural Research, 44, 10–14.Google Scholar
Kellow, NJ, Coughlan, MT, Reid, CM. (2014) Metabolic benefits of dietary prebiotics in human subjects: A systematic review of randomised controlled trials. British Journal of Nutrition, 111, 1147–1161.CrossRefGoogle ScholarPubMed
Kelly, BJ, Tebas, P. (2018) Clinical practice and infrastructure review of faecal microbiota transplantation for Clostridium difficile infection. Chest, 153, 266–277.Google Scholar
Kennedy, J, Baker, P, Piper, C, et al. (2009) Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters. Marine Biotechnology, 11, 384–396.Google Scholar
Kim, J, Choi, GS, Kim, SB, et al. (2006) Screening and characterization of a novel esterase from a metagenomic library. Protein Expression and Purification, 45, 315–323.Google Scholar
Kittelmann, S, Pinares-Patiño, CS, Seedorf, H, et al. (2014) Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS ONE, 9, 1–9.Google Scholar
Kline, KA, Fälker, S, Dahlberg, S, et al. (2009) Bacterial adhesins in host–microbe interactions. Cell Host and Microbe, 5, 580–592.CrossRefGoogle ScholarPubMed
Knauf, M, Moniruzzaman, M. (2004) Lignocellulosic biomass processing: A perspective. International Sugar Journal, 106, 147–150.Google Scholar
Knight, R, Navas, J, Quinn, RA, et al. (2018) Best practices for analysing microbiomes. Nature Reviews Microbiology, 16, 410–422.Google Scholar
Lacey, LA. (2007) Bacillus thuringiensis serovariety israelensis and Bacillus sphaericus for mosquito control. Journal of the American Mosquito Control Association, 23, 133–163.Google Scholar
Lambert, B, Peferoen, M. (1992) Insecticidal promise of Bacillus thuringiensis: Facts and mysteries about a successful biopesticide. Bioscience, 42, 112–122.Google Scholar
Lämmle, K, Zipper, H, Breuer, M, et al. (2007) Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. Journal of Biotechnology, 127, 575–592.Google Scholar
LeBlanc, JG, Aubry, C, Cortes-Perez, NG, et al. (2013) Mucosal targeting of therapeutic molecules using genetically modified lactic acid bacteria: An update. FEMS Microbiology Letters, 344, 1–9.Google Scholar
Lee, CC, Kibblewhite-Accinelli, RE, Wagschal, K, et al. (2006) Cloning and characterization of a cold-active xylanase enzyme from an environmental DNA library. Extremophiles, 10, 295–300.Google Scholar
Lees, RS, Gilles, JR, Hendrichs, J, et al. (2015) Back to the future: The sterile insect technique against mosquito disease vectors. Current Opinion in Insect Science, 10, 156–162.Google Scholar
Lehman, RM, Taheri, WI, Osborne, SL, et al. (2012) Fall cover cropping can increase arbuscular mycorrhizae in soils supporting intensive agricultural production. Applied Soil Ecology, 61, 300–304.Google Scholar
Lennon, JT, Jones, SE. (2011) Microbial seed banks: The ecological and evolutionary implications of dormancy. Nature Reviews Microbiology, 9, 119–130.Google Scholar
Li, LL, McCorkle, SR, Monchy, S, et al. (2009) Bioprospecting metagenomes: Glycosyl hydrolases for converting biomass. Biotechnology for Biofuels, 2, 10.Google Scholar
Lian, J, Wijffels, RH, Smidt, H, et al. (2018) The effect of the algal microbiome on industrial production of microalgae. Microbial Biotechnology, 11, 806–818.Google Scholar
Ligon, BL. (2004) Penicillin: Its discovery and early development. Seminars in Pediatric Infectious Diseases, 15, 52–57.Google Scholar
Lin, J, Zhang, Y, He, C, et al. (2018) Probiotics supplementation in children with asthma: A systematic review and meta-analysis. Journal of Paediatrics and Child Health, 54, 953–961.Google Scholar
Lindemann, SR, Bernstein, HC, Song, HS, et al. (2016) Engineering microbial consortia for controllable outputs. The ISME Journal, 10, 2077–2084.Google Scholar
Ling, LL, Schneider, T, Peoples, AJ, et al. (2015) A new antibiotic kills pathogens without detectable resistance. Nature, 517, 455–459.Google Scholar
Liu, C, Zou, G, Yan, X, et al. (2018b) Screening of multimeric β-xylosidases from the gut microbiome of a higher termite, Globitermes brachycerastes. International Journal of Biological Sciences, 14, 608.Google Scholar
Liu, Y, Li, X, Zhang, L, et al. (2018a) Response of the wheat rhizosphere soil nematode community in wheat/walnut intercropping system in Xinjiang, Northwest China. Applied Entomology and Zoology, 53, 297–306.Google Scholar
Loudon, AH, Woodhams, DC, Parfrey, LW, et al. (2014) Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus). The ISME Journal, 8, 830–840.Google Scholar
Machado, AAS, Valyi, K, Rillig, MC. (2016) Potential environmental impacts of an ‘Underground Revolution’. Trends in Ecology & Evolution, 31, 2016–2018.Google Scholar
Martín, JA, Macaya-Sanz, D. (2015) Strong in vitro antagonism by elm xylem endophytes is not accompanied by temporally stable in planta protection against a vascular pathogen under field conditions. European Journal of Plant Pathology, 142, 185–196.Google Scholar
Martínez Cruz, P, Ibáñez, AL, Monroy Hermosillo, OA, et al. (2012) Use of probiotics in aquaculture. ISRN Microbiology, 2012, 1–13.Google Scholar
McKean, J, Naug, H, Nikbakht, E, et al. (2017) Probiotics and subclinical psychological symptoms in healthy participants: A systematic review and meta-analysis. The Journal of Alternative and Complementary Medicine, 23, 249–258.Google Scholar
McKenzie, VJ, Kueneman, JG, Harris, RN. (2018) Probiotics as a tool for disease mitigation in wildlife: Insights from food production and medicine. Annals of the New York Academy of Sciences, 1429, 18–30.CrossRefGoogle ScholarPubMed
Menendez, E, Garcia-Fraile, P. (2017) Plant probiotic bacteria: Solutions to feed the world. AIMS Microbiology, 3, 747–748.Google Scholar
Middleton, EL, Bever, JD. (2012) Inoculation with a native soil community advances succession in a grassland restoration. Restoration Ecology, 20, 218–226.Google Scholar
Miles, LA, Lopera, CA, González, S, et al. (2012) Exploring the biocontrol potential of fungal endophytes from an Andean Colombian Paramo ecosystem. BioControl, 57, 697–710.Google Scholar
Mills, S, Griffin, C, O’Connor, PM, et al. (2017) A multibacteriocin cheese starter system, comprising nisin and lacticin 3147 in Lactococcus lactis, in combination with plantaricin from Lactobacillus plantarum. Applied and Environmental Microbiology, 83, 1–17.Google Scholar
Mishra, S, Wang, KH, Sipes, BS, et al. (2017) Suppression of root-knot nematode by vermicompost tea prepared from different curing ages of vermicompost. Plant Disease, 101, 734–737.CrossRefGoogle ScholarPubMed
Mitri, S, Foster, KR. (2013) The genotypic view of social interactions in microbial communities. Annual Review of Genetics, 47, 247–273.Google Scholar
Mitter, B, Pfaffenbichler, N, Flavell, R, et al. (2017) A new approach to modify plant microbiomes and traits by introducing beneficial bacteria at flowering into progeny seeds. Frontiers in Microbiology, 8, 1–10.Google Scholar
Mousa, WK, Raizada, MN. (2015) Biodiversity of genes encoding anti-microbial traits within plant associated microbes. Frontiers in Plant Science, 6, 231.CrossRefGoogle ScholarPubMed
Mousa, WK, Shearer, CR, Limay-Rios, V, et al. (2015) Bacterial endophytes from wild maize suppress Fusarium graminearum in modern maize and inhibit mycotoxin accumulation. Frontiers in Plant Science, 6, 1–19.Google Scholar
Mu, J, Li, X, Jiao, J, et al. (2017) Biocontrol potential of vermicompost through antifungal volatiles produced by indigenous bacteria. Biological Control, 112, 49–54.Google Scholar
Mudroňová, D, Toporčák, J, Nemcová, R, et al. (2011) Lactobacillus sp. as a potential probiotic for the prevention of Paenibacillus larvae infection in honey bees. Journal of Apicultural Research, 50, 323–324.Google Scholar
Mueller, UG, Sachs, JL. (2015) Engineering microbiomes to improve plant and animal health. Trends in Microbiology, 23, 1–12.Google Scholar
Muletz, CR, Myers, JM, Domangue, RJ, et al. (2012) Soil bioaugmentation with amphibian cutaneous bacteria protects amphibian hosts from infection by Batrachochytrium dendrobatidis. Biological Conservation, 152, 119–126.Google Scholar
Müller, CA, Obermeier, MM, Berg, G. (2016) Bioprospecting plant-associated microbiomes. Journal of Biotechnology, 235, 171–180.Google Scholar
Naik, S, Bouladoux, N, Wilhelm, C, et al. (2012) Compartmentalized control of skin immunity by resident commensals. Science, 337, 1115–1119.Google Scholar
Neu, J, Rushing, J. (2011) Cesarean versus vaginal delivery: Long-term infant outcomes and the hygiene hypothesis. Clinics in Perinatology, 38, 321–331.Google Scholar
Nunes, RV, Scherer, C, Pozza, PC, et al. (2012) Use of probiotics to replace antibiotics for broilers. Revista Brasileira de Zootecnia, 41, 2219–2224.Google Scholar
Ohkuma, M. (2003) Termite symbiotic systems: Efficient bio-recycling of lignocellulose. Applied Microbiology and Biotechnology, 61, 1–9.Google Scholar
Oldroyd, GED. (2013) Speak, friend, and enter: Signalling systems that promote beneficial symbiotic associations in plants. Nature Reviews Microbiology, 11, 252–263.Google Scholar
Ouwehand, AC, Salminen, S, Ouwehand, AC, et al. (2009) In vitro adhesion assays for probiotics and their in vivo relevance: A review. Microbial Ecology in Health and Disease, 15, 175–184.Google Scholar
Pandey, G, Pandey, AK, Pandey, SS, et al. (2018) Microbiota in immune pathogenesis and the prospects for pre and probiotic dietetics in psoriasis. Biomedical Research Journal, 2, 220.Google Scholar
Pătruică, S, Mot, D. (2012) The effect of using prebiotic and probiotic products on intestinal micro-flora of the honeybee (Apis mellifera carpatica). Bulletin of Entomological Research, 102, 619–623.Google Scholar
Pershina, E, Valkonen, J, Kurki, P, et al. (2015) Comparative analysis of prokaryotic communities associated with organic and conventional farming systems. PLoS ONE, 10, 1–16.CrossRefGoogle ScholarPubMed
Petrof, EO, Gloor, GB, Vanner, SJ, et al. (2013) Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome, 1, 3.Google Scholar
Petrosillo, N, Granata, G, Cataldo, MA. (2018) Novel antimicrobials for the treatment of Clostridium difficile infection. Frontiers in Medicine, 5, 1–16.Google Scholar
Piovia-Scott, J, Rejmanek, D, Woodhams, DC, et al. (2017) Greater species richness of bacterial skin symbionts better suppresses the amphibian fungal pathogen Batrachochytrium dendrobatidis. Microbial Ecology, 74, 217–226.Google Scholar
Poelchau, MF, Coates, BS, Childers, CP, et al. (2016) Agricultural applications of insect ecological genomics. Current Opinion in Insect Science, 13, 61–69.Google Scholar
Pohjanen, J, Koskimäki, JJ, Sutela, S, et al. (2014) Interaction with ectomycorrhizal fungi and endophytic Methylobacterium affects nutrient uptake and growth of pine seedlings in vitro. Tree Physiology, 34, 993–1005.Google Scholar
Ptaszyńska, AA, Borsuk, G, Zdybicka-Barabas, A, et al. (2016) Are commercial probiotics and prebiotics effective in the treatment and prevention of honeybee nosemosis C? Parasitology Research, 115, 397–406.Google Scholar
Quaye, AK, Volk, TA, Hafner, S, et al. (2011) Impacts of paper sludge and manure on soil and biomass production of willow. Biomass and Bioenergy, 35, 2796–2806.Google Scholar
Quiza, L, St-Arnaud, M, Yergeau, E, et al. (2015) Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. Frontiers in Plant Science, 6, 1–11.Google Scholar
Rana, V, Rana, D. (2017) Role of microorganisms in lignocellulosic biodegradation. In: Renewable Biofuels: Bioconversion of Lignocellulosic Biomass by Microbial Community. Cham: Springer.Google Scholar
Rebollar, EA, Antwis, RE, Becker, MH, et al. (2016) Using ‘omics’ and integrated multi-omics approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases. Frontiers in Microbiology, 7, 68.Google Scholar
Redford, KH, Adams, W, Mace, GM. (2013) Synthetic biology and conservation of nature: Wicked problems and wicked solutions. PLoS Biology, 11, 2–5.Google Scholar
Redman, RS, Dunigan, D, Rodriguez, RJ, et al. (2001) Fungal symbiosis from mutualism to parasitism: Who controls the outcome, host or invader? New Phytologist, 151, 705–716.Google Scholar
Rees, HC, Grant, S, Jones, B, et al. (2003) Detecting cellulase and esterase enzyme activities encoded by novel genes present in environmental DNA libraries. Extremophiles, 7, 415–421.Google Scholar
Reich, I, Ijaz, UZ, Gormally, M, et al. (2018) 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Scientific Reports, 8, 10402.Google Scholar
Remans, R, Ramaekers, L, Schelkens, S, et al. (2008) Effect of Rhizobium–Azospirillum coinoculation on nitrogen fixation and yield of two contrasting Phaseolus vulgaris L. genotypes cultivated across different environments in Cuba. Plant and Soil, 312, 25–37.Google Scholar
Richardson, TH, Tan, X, Frey, G, et al. (2002) A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase. Journal of Biological Chemistry, 277, 26,501–26,507.Google Scholar
Ripple, WJ, Wolf, C, Newsome, TM, et al. (2017) World scientists warning to humanity: A second notice. BioScience, 67, 1026–1028.Google Scholar
Roehe, R, Dewhurs, RJ, Duthie, CA, et al. (2016) Bovine host genetic variation influences rumen microbial methane production with best selection criterion for low methane emitting and efficiently feed converting hosts based on metagenomic gene abundance. PLoS Genetics, 12, e1005846.Google Scholar
Rudrappa, T, Czymmek, KJ, Pare, PW, et al. (2008) Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiology, 148, 1547–1556.Google Scholar
Sáez, D, Fernández, P, Rivera, A, et al. (2012) Oral immunization of mice with recombinant Lactococcus lactis expressing Cu, Zn superoxide dismutase of Brucella abortus triggers protective immunity. Vaccine, 30, 1283–1290.Google Scholar
Saez-Lara, MJ, Gomez-Llorente, C, Plaza-Diaz, P, et al. (2015) The role of probiotic lactic acid bacteria and bifidobacteria in the prevention and treatment of inflammatory bowel disease and other related diseases: A systematic review of randomized human clinical trials. BioMed Research International, 2015, 505878.Google Scholar
Salazar, A, Sulman, BN, Dukes, JS. (2018) Microbial dormancy promotes microbial biomass and respiration across pulses of drying-wetting stress. Soil Biology and Biochemistry, 116, 237–244.Google Scholar
Sander, JD, Joung, JK. (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nature Biotechnology, 32, 347–350.Google Scholar
Sarma, BK, Yadav, SK, Singh, S, et al. (2015) Microbial consortium-mediated plant defense against phytopathogens: Readdressing for enhancing efficacy. Soil Biology and Biochemistry, 87, 25–33.Google Scholar
Scheuring, I, Yu, DW. (2012) How to assemble a beneficial microbiome in three easy steps. Ecology Letters, 15, 1300–1307.Google Scholar
Schmidt, JE, Bowles, TM, Gaudin, ACM. (2016) Using ancient traits to convert soil health into crop yield: Impact of selection on maize root and rhizosphere function. Frontiers in Plant Science, 7, 1–11.Google Scholar
Schweitzer, JA, Bailey, JK, Fischer, DG, et al. (2008) Plant–soil–microorganism interactions: Heritable relationship between plant genotype and associated soil microorganisms. Ecology, 89, 773–781.Google Scholar
Scully, ED, Geib, SM, Hoover, K, et al. (2013) Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. PLoS ONE, 8,e73827.Google Scholar
Seshadri, R, Leahy, SC, Attwood, GT, et al. (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 collection. Nature Biotechnology, 36, 359–367.Google Scholar
Sheth, RU, Cabral, V, Chen, SP, et al. (2016) Manipulating bacterial communities by in situ microbiome engineering. Trends in Genetics, 32, 189–200.Google Scholar
Shi, W, Ding, SY, Yuan, JS. (2011) Comparison of insect gut cellulase and xylanase activity across different insect species with distinct food sources. Bioenergy Research, 4, 1–10.CrossRefGoogle Scholar
Shi, W, Xie, S, Chen, X, et al. (2013) Comparative genomic analysis of the endosymbionts of herbivorous insects reveals eco-environmental adaptations: Biotechnology applications. PLoS Genetics, 9, e1003131.CrossRefGoogle Scholar
Shin, JM, Gwak, JW, Kamarajan, P, et al. (2016) Biomedical applications of nisin. Journal of Applied Microbiology, 120, 1449–1465.Google Scholar
Silva, CO, Vaz, RP, Filho, EX. (2018) Bringing plant cell wall‐degrading enzymes into the lignocellulosic biorefinery concept. Biofuels, Bioproducts and Biorefining, 12, 277–289.Google Scholar
Sleeman, JM. (2013) Has the time come for big science in wildlife health? EcoHealth, 10, 335–338.Google Scholar
Stacy, A, McNally, L, Darch, SE, et al. (2016) The biogeography of polymicrobial infection. Nature Reviews Microbiology, 14, 93–105.Google Scholar
Stecher, B, Chaffron, S, Käppeli, R, et al. (2010) Like will to like: Abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathogens, 6, e1000711.Google Scholar
Stephens, PR, Altizer, S, Smith, KF, et al. (2016) The macroecology of infectious diseases: A new perspective on global-scale drivers of pathogen distributions and impacts. Ecology Letters, 19, 1159–1171.Google Scholar
Sun, J, Buys, NJ. (2016) Glucose- and glycaemic factor-lowering effects of probiotics on diabetes: A meta-analysis of randomised placebo-controlled trials. British Journal of Nutrition, 115, 1167–1177.Google Scholar
Tabashnik, BE. (1994) Evolution of resistance to Bacillus thuringiensis. Annual Review of Entomology, 39, 47–79.Google Scholar
Tang, KL, Caffrey, NP, Nóbrega, DB, et al. (2017) Articles restricting the use of antibiotics in food-producing animals and its associations with antibiotic resistance in food-producing animals and human beings: A systematic review and meta-analysis. The Lancet, 5196, 9–11.Google Scholar
Thijs, S, Sillen, W, Rineau, F, et al. (2016) Towards an enhanced understanding of plant–microbiome interactions to improve phytoremediation: Engineering the metaorganism. Frontiers in Microbiology, 7, 1–15.Google Scholar
Thushara, RM, Gangadaran, S, Solati, Z, et al. (2016) Cardiovascular benefits of probiotics: a review of experimental and clinical studies. Food and Function, 7, 632–642.Google Scholar
Timmerman, HM, Rutten, NBMM, Boekhorst, J, et al. (2017) Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures. Scientific Reports, 7, 1–10.Google Scholar
Tompkins, DM, Carver, S, Jones, ME, et al. (2015) Emerging infectious diseases of wildlife: A critical perspective. Trends in Parasitology, 31, 149–159.Google Scholar
Tuomisto, HL. (2019) The complexity of sustainable diets. Nature Ecology and Evolution, 3, 720–721.Google Scholar
Trivedi, P, Delgado-Baquerizo, M, Trivedi, C, et al. (2016) Microbial regulation of the soil carbon cycle: Evidence from gene–enzyme relationships. The ISME Journal, 10, 2593–2604.Google Scholar
Udwary, DW, Zeigler, L, Asolkar, RN, et al. (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proceedings of the National Academy of Sciences, 104, 10376–10381.Google Scholar
Uyeno, Y, Shigemori, S, Shimosato, T. (2015) Effect of probiotics/prebiotics on cattle health and productivity. Microbes and Environments, 30, 126–132.Google Scholar
van Elsas, JD, Chiurazzi, M, Mallon, CA, et al. (2012) Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences, 109, 1159–1164.Google Scholar
Varjani, SJ. (2017) Microbial degradation of petroleum hydrocarbons. Bioresource Technology, 223, 277–286.Google Scholar
Venugopalan, V, Shriner, KA, Wong-Beringer, A. (2010) Regulatory oversight and safety of probiotic use. Emerging Infectious Diseases, 16, 1661–1665.Google Scholar
Verbeken, G, Huys, I, Pirnay, JP, et al. (2014) Taking bacteriophage therapy seriously: A moral argument. BioMed Research International, 2014, 1–8.Google Scholar
Viikari, L, Vehmaanperä, J, Koivula, A. (2012) Lignocellulosic ethanol: From science to industry. Biomass and Bioenergy, 46, 13–24.Google Scholar
Voget, S, Leggewie, C, Uesbeck, A, et al. (2003) Prospecting for novel biocatalysts in a soil metagenome. Applied and Environmental Microbiology, 69, 6235–6242.Google Scholar
Voget, S, Steele, HL, Streit, WR. (2006) Characterization of a metagenome-derived halotolerant cellulase. Journal of Biotechnology, 126, 26–36.Google Scholar
Vosátka, M, Látr, A, Gianinazzi, S, et al. (2012) Development of arbuscular mycorrhizal biotechnology and industry: Current achievements and bottlenecks. Symbiosis, 58, 29–37.Google Scholar
Walder, F, Van Der Heijden, MGA. (2015) Regulation of resource exchange in the arbuscular mycorrhizal symbiosis. Nature Plants, 1, 1–7.Google Scholar
Walke, JB, Belden, LK. (2016) Harnessing the microbiome to prevent fungal infections: Lessons from amphibians. PLoS Pathogens, 12, e1005796.Google Scholar
Walters, WA, Jin, Z, Youngblut, N, et al. (2018) Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proceedings of the National Academy of Sciences, 115, 7368–7373.Google Scholar
Wang, S, Xu, M, Wang, W, et al. (2016) Systematic review: Adverse events of fecal microbiota transplantation. PLoS ONE, 11, e0161174.Google Scholar
Warnecke, F, Luginbühl, P, Ivanova, N, et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 450, 560.Google Scholar
Watanabe, H, Tokuda, G. (2010) Cellulolytic systems in insects. Annual Review of Entomology, 55, 609–632.Google Scholar
Wei, Z, Yang, T, Friman, VP, et al. (2015) Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health. Nature Communications, 6, 8413.Google Scholar
Weimer, PJ, Stevenson, DM, Mantovani, HC, et al. (2010) Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents. Journal of Dairy Science, 93, 5902–5912.Google Scholar
Wescombe, PA, Hale, JD, Heng, NC, et al. (2012) Developing oral probiotics from Streptococcus salivarius. Future Microbiology, 7, 1355–1371.Google Scholar
Williams, RJ, Howe, A, Hofmockel, KS. (2014) Demonstrating microbial co-occurrence pattern analyses within and between ecosystems. Frontiers in Microbiology, 5, 1–10.Google Scholar
Wohlleben, W, Mast, Y, Stegmann, E, et al. (2016) Antibiotic drug discovery. Microbial Biotechnology, 9, 541–548.Google Scholar
Wong, WS, Tan, SN, Ge, L, et al. (2016) The importance of phytohormones and microbes in biostimulants: Mass spectrometric evidence and their positive effects on plant growth. Acta Horticulturae, 1148, 49–60.Google Scholar
Woodhams, DC, Geiger, CC, Reinert, LK, et al. (2012) Treatment of amphibians infected with chytrid fungus: Learning from failed trials with itraconazole, antimicrobial peptides, bacteria, and heat therapy. Diseases of Aquatic Organisms, 98, 11–25.Google Scholar
Xu, C, Arancon, RAD, Labidi, J, et al. (2014) Lignin depolymerisation strategies: Towards valuable chemicals and fuels. Chemical Society Reviews, 43, 7485–7500.Google Scholar
Yáñez-Ruiz, DR, Abecia, L, Newbold, CJ. (2015) Manipulating rumen microbiome and fermentation through interventions during early life: A review. Frontiers in Microbiology, 6, 1–12.Google Scholar
Yun, J, Kang, S, Park, S, et al. (2004) Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Applied and Environmental Microbiology, 70, 7229–7235.Google Scholar
Zasloff, M. (2002) Antimicrobial peptides of multicellular organisms. Nature, 415, 389–395.Google Scholar
Zee, PC, Bever, JD. (2014) Joint evolution of kin recognition and cooperation in spatially structured rhizobium populations. PLoS ONE, 9, e95141.Google Scholar
Zhang, NN, Sun, YM, Li, L, et al. (2010) Effects of intercropping and Rhizobium inoculation on yield and rhizosphere bacterial community of faba bean (Vicia faba L.). Biology and Fertility of Soils, 46, 625–639.Google Scholar
Zhang, GQ, Hu, HJ, Liu, CY,et al. (2016) Probiotics for prevention of atopy and food hypersensitivity in early childhood: A PRISMA-compliant systematic review and meta-analysis of randomized controlled trials. Medicine (Baltimore), 95, 1–10.Google Scholar
Zhang, Q, Yu, Y, Velasquez, JE, et al. (2012) Evolution of lanthipeptide synthetases. Proceedings of the National Academy of Sciences, 109, 18361–18366.Google Scholar
Zhao, K, Penttinen, P, Guan, T, et al. (2011) The diversity and anti-microbial activity of endophytic actinomycetes isolated from medicinal plants in Panxi Plateau, China. Current Microbiology, 62, 182–190.Google Scholar
- 1
- Cited by