Journals A-Z
All Subjects
Free Journals
sciepub.com
Applied Ecology and Environmental Sciences
ISSN (Print): 2328-3912 ISSN (Online): 2328-3920 Website: https://www.sciepub.com/journal/aees Editor-in-chief: Alejandro González Medina
Open Access
Journal Browser
Go
Issue 10, Volume 9
Article Metrics
  • 5829
    Views
  • 7211
    Saves
  • 0
    Citations
  • 0
    Likes
Export Article
Applied Ecology and Environmental Sciences. 2021, 9(10), 865-872
DOI: 10.12691/aees-9-10-3
Open AccessReview Article

Microbiome Engineering and Its Applications: A Rapid Review

Gemechu Berhanu1, Vikram Godishala2 and Venkataramana Kandi3,

1College of Agriculture and Veterinary Medicine, Dambi Dollo University, Ethiopia

2Department of Biotechnology, Ganapthi Degree College, Parakal, Telangana, India

3Department of Microbiology, Prathima Institute of Medical Sciences, Karimnagar, Telangana, India

Pub. Date: October 14, 2021
View Full Text Full Text PDF (203 KB) Full Text ePUB(43 KB)

Cite this paper:
Gemechu Berhanu, Vikram Godishala and Venkataramana Kandi. Microbiome Engineering and Its Applications: A Rapid Review. Applied Ecology and Environmental Sciences. 2021; 9(10):865-872. doi: 10.12691/aees-9-10-3

Abstract

The microbiome is a multifarious and dynamic ecological element, in which different species such as bacteria, fungi, archaea, protozoa, and viruses are in continual flux. They can alter host development, the physiology, and systemic defenses that play a great role in food producing animals. Perturbation to the microbiota or dysbiosis affects greatly the host’s normal physiology and may cause different diseases in the host. Microbiomes can be studied in different ways including different molecular techniques and omics technologies. Microbiome engineering is an experimental method that improves host performance by artificially selecting for microbial communities with specific effects on host fitness. Different methods are used in microbiome engineering and these include synthetic biology, modulating the microbiota, antibiotics, feed enzymes, prebiotics, probiotics, fecal microbiota transplantation, horizontal gene transfer, acceptance, and maintenance of foreign DNA, and genome editing. All these methods participate in the manipulation of the genomic content of microbiomes. This technique has different advantages including treatment mental health problems, modulating host immunity, improving nutrition, modifying physiology of the hosts and the characteristics of the ecosystems where they reside, modulates the pathogenesis, progression, and treatment of diseases, improving agricultural productivity, controls the variability for the efficiency of feed utilization in ruminants. Therefore, engineering microbiomes has a great advantage in improving the production systems of livestock.

Keywords:
Microbiome ecology engineering improvements livestock production

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

References:

[1]  Morgavi DP, Kelly WJ, Janssen PH, Attwood GT. Rumen microbial (meta) genomics and its application to ruminant production. Animal. 2013; 7: 184-201.
 
[2]  Morgavi DP, Forano E, Martin C, Newbold CJ. Microbial ecosystem and methanogenesis in ruminants. Animal. 2012; 6(5): 871.
 
[3]  Matthews C, Crispie F, Lewis E, Reid M, O’Toole PW, Cotter PD. The rumen microbiome a crucial consideration when optimizing milk and meat production and nitrogen utilisation efficiency. Gut Microb. 2019; 10(2): 115-132.
 
[4]  Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Rev Microbiol. 2008; 6: 776-788.
 
[5]  Stein RR, Bucci V, Toussaint NC, et al. Ecological modeling from time-series inference: Insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol. 2013; 9(12), e1003388.
 
[6]  Coyte K, Schluter J, Foster K. The ecology of the microbiome: networks, competition and stability. Science. 2015; 350: 663-666.
 
[7]  Hall A, Tolonen AC, Xavier RJ. Human genetic variation and the gut microbiome in disease. Nat Publ Gr. 2017; 18.
 
[8]  Delgado B, Bach A, Guasch I. Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle. Scientific Reports, 2019; 9: 11.
 
[9]  Medina M, Sachs JL. Symbiont genomics, our new tangled bank. Genomics. 2010; 95: 129-137.
 
[10]  Mueller UG, Sacchs JL. Engineering Microbiomes to Improve Plant and Animal Health. Trends Microbiol. 2015; 23(10): 606-617.
 
[11]  Morowitz MJ, Carlisle EM, Alverdy JC. Contributions of intestinal bacteria to nutrition and metabolism in the critically ill. Surgical Clin N Am. 2011; 91(4): 771-785.
 
[12]  Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009; 9: 313-323.
 
[13]  Brulc JM, Antonopoulos DA, Miller ME, et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci., 2009; 106(6): 1948-1953.
 
[14]  McCann JC, Luan S, Cardoso FC, Derakhshani H, Khafipour E, Loor JJ. Induction of subacute ruminal acidosis affects the ruminal microbiome and epithelium. Front Microbiol. 2016; 7: 701.
 
[15]  Myer PR, Smith TP, Wells JE, Kuehn LA, Freetly HC. Rumen microbiome from steers differing in feed efficiency. PLoS One, 2015; 10(6): e0129174.
 
[16]  Clemmons BA, Voy BH, Myer PR. Altering the Gut Microbiome of Cattle: Considerations of Host-Microbiome Interactions for Persistent Microbiome Manipulation. 2018.
 
[17]  Yadav R, Kumar V, Baweja M, Shukla P. Gene editing and genetic engineering approaches for advanced probiotics: A review. Critical Reviews in Food Science and Nutrition, 2018; 58(10): 1735-1746.
 
[18]  Huttenhower C, Gevers D, Knight R, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486: 207-214.
 
[19]  Belizârio JE, Napolitano, M. Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches. Front Microbiol. 2015; 6: 1050.
 
[20]  Shen J, Obin MS, Zhao L. The gut microbiota, obesity and insulin resistance. Mol Aspects Med. 2013; 34(1): 39-58.
 
[21]  Naseer MI, Bibi F, Alqahtani MH, Chaudhary AG, Azhar EI, Kamal MA, Yasir M. Role of gut microbiota in obesity, type 2 diabetes and Alzheimer’s disease. CNS and Neurological Disorders - Drug Targets, 2014; 13(2): 305-311.
 
[22]  Azcarate-Peril MA, Sikes M, Bruno-Barcena JM. The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? Am J Physiol Gastrointest Liver Physiol. 2011; 301(3): G401-24.
 
[23]  Panzer AR, Lynch SV. Influence and effect of the human microbiome in allergy and asthma. Curr Opin Rheumatol. 2015; 27(4): 373-80.
 
[24]  Barlow GM, Yu A, Mathur R. Role of the Gut Microbiome in Obesity and Diabetes Mellitus. Nutr. Clin. Pract. 2015; 30: 787-797.
 
[25]  Sobhani I, Tap J, Roudot-Thoraval F, et al. Microbial dysbiosis in colorectal cancer (CRC) patients. PloS one, 2011; 6(1): e16393.
 
[26]  Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015; 26: 26191.
 
[27]  Gevers D, Kugathasan S, Denson LA, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell host Microb. 2014; 15(3): 382-92.
 
[28]  El-Aidy S, Kleerebezem M. Molecular signatures for the dynamic process of establishing intestinal host-microbial homeostasis: potential for disease diagnostics? Curr Opin Gastroenterol. 2013; 29(6): 621-627.
 
[29]  Franzosa EA, Morgan XC, Segata N, et al. Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences. 2014; 111(22): E2329-38.
 
[30]  Tsai YT, Cheng PC, Pan TM. Anti-obesity effects of gut microbiota are associated with lactic acid bacteria. Appl. Microbiol. Biotechnol, 2014; 98: 1-10.
 
[31]  Cribby S, Taylor M, Reid G. Vaginal microbiota and the use of probiotics. Interdiscip. Perspect. Infect. Dis, 2008; 256490.
 
[32]  Blaut M, Collins MD, Welling GW, Dore J, Van Loo J, de Vos W. Molecular biological methods for studying the gut microbiota: the EU human gut flora project. British Journal of Nutrition. 2002; 87(S2): S203-11.
 
[33]  Arnold JW, Roach J, Azcarate-Peril MA. Emerging technologies for gut microbiome research. Trends in microbiology. 2016; 24(11): 887-901.
 
[34]  Bashiardes S, Zilberman-Schapira G, Elinav E. Use of metatranscriptomics in microbiome research. Bioinformatics and biology insights. 2016; BBI-S34610.
 
[35]  Inda ME, Broset E, Lu TK, de la Fuente-Nunez C. Emerging frontiers in microbiome engineering. Trends in immunology. 2019; 40(10): 952-73.
 
[36]  Gosalbes MJ, Durbán A, Pignatelli M, et al. Metatranscriptomic approach to analyze the functional human gut microbiota. PloS one. 2011; 6(3): e17447.
 
[37]  Peano C, Pietrelli A, Consolandi C, et al. An efficient rRNA removal method for RNA sequencing in GC-rich bacteria. Microb Inform Exp. 2013; 3(1): 1.
 
[38]  Lawson CE, Harcombe WR, Hatzenpichler R, et al. Common principles and best practices for engineering microbiomes. Nature Rev Microbiol. 2019; 17(12): 725-741.
 
[39]  Van Pijkeren J-P, Neoh KM, Sirias D, Findley AS, Britton RA. Exploring optimization parameters to increase ssDNA recombineering in Lactococcus lactis and Lactobacillus reuteri. Bioengineered, 2012; 3: 209-17.
 
[40]  Foo JL, Ling H, Lee YS, Chang MW. Microbiome engineering: Current applications and its future. Biotechnol J. 2017; 12(3): 1600099.
 
[41]  Bober JR, Beisel CL, Nair NU. Synthetic biology approaches to engineer probiotics and members of the human microbiota for biomedical applications. Annual review of biomedical engineering. 2018; 20: 277-300.
 
[42]  Lagier J-C, Khelaifia S, AIou MT, et al. Culture of previously uncultured members of the human gut microbiota by eulturomies. Nat Microbiol. 2016; 1: 1-8
 
[43]  Waller MC, Bober JR, Nair NU, Beisei CL. Toward a genetic tool development pipeline for host-associated bacteria. Curr Opin Microbiol. 2017; 38: 156-64.
 
[44]  Marchand N, Collins CH. Synthetic quorum sensing and cell-cell communication in gram-positive Bacillus megaterium. ACS Synth Biol. 2016; 5: 597-606.
 
[45]  Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods. 2014; 11: 508-20.
 
[46]  Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014; 157: 1262-78.
 
[47]  Park M, Tsai SL, Chen W. Microbial biosensors: engineered microorganisms as the sensing machinery. Sensors, 2013; 3: 5777-5795
 
[48]  Rong G, Corrie SR, Clark HA. In vivo biosensing: progress and perspectives. ACS Sens. 2017; 2: 327-38.
 
[49]  Mimee M. Genetic Technologies to Engineer and Understand the Microbiome. PhD Thesis, Massachusetts Institute of Technology, 2018.
 
[50]  Cameron DE, Bashor CJ, and Collins JJ. A brief history of synthetic biology. Nat Rev Microbiol. 2014; 12: 381-90.
 
[51]  Ullah MW, Khattak WA, Ul-Islam M, Khan S, Park JK. Metabolic engineering of synthetic cell-free systems: strategies and applications. Biochem Eng J. 2016; 105: 391M-05.
 
[52]  Landry BP, Tabor JJ. Engineering diagnostic and therapeutic gut bacteria. Microbiol Spectr. 2017; 5: 5.
 
[53]  Schultz M, Watzl S, Oelschlaeger TA, et al. Green fluorescent protein for detection of the probiotic microorganism Escherichia coli strain Nissle 1917 (EcN) in vivo. J Microbiol Methods. 2005; 61(3): 389-398.
 
[54]  Isabella VM, Ha BN, Castillo M, et al. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nature Biotechnol. 2018; 36(9): 857-864.
 
[55]  Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nature Rev Microbiol. 2016; 14(1): 20-32.
 
[56]  Shen N, Sheth RU, Cabral V, Chen SP, Wang HH. Manipulating bacterial communities by in situ microbiome engineering. Trends Gen. 2016; 32(4): 189-200.
 
[57]  Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med. 2016; 8: 39.
 
[58]  Van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. New England J Med. 2013; 368(5): 407-15.
 
[59]  Sheth RU, Cabral V, Chen SP, Wang HH. Manipulating bacterial communities by in situ microbiome engineering. Trends Genet. 2016; 32: 189-200.
 
[60]  Pal M, Kerorsa GB, Marami LM, Kandi V. Epidemiology, pathogenicity, animal infections, antibiotic resistance, public health significance, and economic impact of Staphylococcus aureus: a comprehensive review. Am J Public Health Res. 2020; 8(1): 14-21.
 
[61]  Van Staden AD, Heunis T, Smith C, Deane S, Dicks LM. Efficacy of lantibiotic treatment of Staphylococcus aureus-induced skin infections, monitored by in vivo bioluminescent imaging. Antimicrob Agents Chemo. 2016; 60(7): 3948-55.
 
[62]  Kingwell K, Bacteriophage therapies reenter clinical trials. Nat Rev Drug Discov. 2015; 14: 515-516.
 
[63]  Kiarie E, Romero LF, Nyachoti CM, The role of added feed enzymes in promoting gut health in swine and poultry. Nutr Res Rev. 2013; 26: 71-88.
 
[64]  Kolodziejczyk AA, Zheng D, Elinav E. Diet–microbiota interactions and personalized nutrition. Nature Rev. 2019; 17: 742-753.
 
[65]  Sanders ME, Gibson GR, Gill HS, Guarner F. Probiotics: their potential to impact human health. Council for Agricultural Science and Technology Issue Paper. 2007; 36: 1-20.
 
[66]  Bustamante M, Oomah BD, Oliveira WP, Burgos-Díaz C, Rubilar M, Shene C. Probiotics and prebiotics potential for the care of skin, female urogenital tract, and respiratory tract. Folia microbiologica. 2020; 65(2): 245-64.
 
[67]  Pandey KR, Naik SR, Vakil BV. Probiotics, prebioties and synbioties—a review. J Food Sei Technol. 2015; 52: 7577-87.
 
[68]  Mattila E, Uusitalo–Seppälä R, Wuorela M, et al. Fecal transplantation, through colonoscopy, is effective therapy for recurrent Clostridium difficile infection. Gastroenterology. 2012; 142(3): 490-496.
 
[69]  Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis : Off Publ Infect Dis Soc Am. 2011; 53: 994-1002.
 
[70]  Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection. Jama. 2014; 312(17): 1772-8..
 
[71]  Lee WJ, Lattimer LD, Stephen S, Borum ML, Doman DB. Fecal microbiota transplantation: a review of emerging indications beyond relapsing clostridium difficile toxin colitis. Gastroenterology & hepatology. 2015; 11(1): 24.
 
[72]  Damman CJ, Miller SI, Surawicz CM, Zisman TL. The microbiome and inflammatory bowel disease: is there a therapeutic role for fecal microbiota transplantation? Am J Gastroenterol. 2012; 107: 1452-9.
 
[73]  Brito IL, Yilmaz S, Huang K, Xu L, et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature, 2016; 535: 435-39.
 
[74]  Kanchiswamy CN, Maffei M, Malnoy M, Velasco R, Kim JS. Fine-tuning next-generation genome editing tools. Trends Biotechnol. 2016; 34: 562-574.
 
[75]  Hale CR, Majumdar S, Elmore J, et al. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Molecular Cell. 2012; 45(3): 292-302.
 
[76]  Sontheimer E, Barrangou R. The bacterial origins of the CRISPR genome editing revolution. Hum. Gene Ther. 2015; 26: 413-424.
 
[77]  Hidalgo-Cantabrana C, O’Flaherty S, Barrangou R. CRISPR-based engineering of next-generation lactic acid bacteria. Current opinion in microbiology. 2017; 37: 79-87.
 
[78]  Mimee M, Tucker AC, Voigt CA, Lu TK. Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell systems. 2015; 1(1): 62-71.
 
[79]  Selle K, Klaenhammer TR, Barrangou R. CRISPR-based screening of genomic island excision events in bacteria. Proceedings of the National Academy of Sciences. 2015; 112(26): 8076-81.
 
[80]  Oh JH, van Pijkeren JP. CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic acids research. 2014; 42(17): e131.
 
[81]  Van Pijkeren JP, Britton RA. Precision genome engineering in lactic acid bacteria. Microbial cell factories. 2014; 13(1): 1-0.
 
[82]  Cryan JF, Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behavior. Nature Reviews Neuroscience, 2012; 13: 701-712.
 
[83]  Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. science. 2012; 336(6086): 1268-1273.
 
[84]  Ridaura VK, Faith JJ, Rey FE, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013; 341(6150).
 
[85]  Hacquard S, Garrido-Oter R, González A, et al. Microbiota and host nutrition across plant and animal kingdoms. Cell host & microbe. 2015; 17(5): 603-16.
 
[86]  Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015; 517(7533): 205-8.
 
[87]  Le Chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013; 500(7464): 541-6.
 
[88]  Kaźmierczak-Siedlecka K, Vitale E, Makarewicz W. COVID-19 - gastrointestinal and gut microbiota-related aspects. Eur Rev Med Pharmacol Sci. 2020 Oct; 24(20): 10853-10859.
 
[89]  Dhar D, Mohanty A. Gut microbiota and Covid-19- possible link and implications. Virus Res. 2020; 285: 198018.
 
[90]  Aktas B, Aslim B. Gut-lung axis and dysbiosis in COVID-19. Turk J Biol. 2020 Jun 21; 44(3): 265-272.
 
[91]  Ferreira C, Viana SD, Reis F. Gut Microbiota Dysbiosis-Immune Hyperresponse-Inflammation Triad in Coronavirus Disease 2019 (COVID-19): Impact of Pharmacological and Nutraceutical Approaches. Microorganisms. 2020; 8(10): 1514. Published 2020 Oct 1.
 
[92]  Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS, Ng SC. Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization. Gastroenterology. 2020 Sep; 159(3): 944-955. e8.
 
[93]  Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L, Li L. Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza. Clin Infect Dis. 2020 Jun 4:ciaa709.
 
[94]  Chen X, Liao B, Cheng L, et al. The microbial coinfection in COVID-19. Appl Microbiol Biotechnol. 2020; 104(18): 7777-7785.
 
[95]  Zuo T, Zhan H, Zhang F, et al. Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge. Gastroenterology. 2020; 159(4): 1302-1310.e5.
 
[96]  Akour A. Probiotics and COVID-19: is there any link? Lett Appl Microbiol. 2020 Sep; 71(3): 229-234.
 
[97]  Bottari B, Castellone V, Neviani E. Probiotics and Covid-19. Int J Food Sci Nutr. 2020 Aug 12: 1-7.
 
[98]  Ramana KV, Mohanty SK. Opportunistic intestinal parasites and TCD4+ cell counts in human immunodeficiency virus seropositive patients. J Med Microbiol. 2009 Dec; 58(Pt 12): 1664-1666.
 
Manuscript template