Advertisement

Shared Microbiome in Different Ecosystems: A Meta-Omics Perspective

  • Arghavan AlisoltaniEmail author
  • Akebe Luther King Abia
  • Linda Bester
Chapter

Abstract

Recent progress in the sequencing technologies and other omics approaches have had a profound impact on microbiology and helped to develop a more complete picture of the microbial composition and function of different ecosystems. One of the observations from meta-omics research is some microbes are ubiquitous in diverse ecosystems and that such shared microbiota could act as a backbone to support ecosystem function. This chapter describes current meta-omics projects studying this issue and addresses the potential of publicly available data to (i) identify the shared microbes that inhabit different environments and to (ii) study the microbial-core functions. We also discuss key challenges, gaps, and perspectives of meta-omic studies to help researchers to take the next steps forward.

Keywords

Core function Meta-omics Microbiota Shared microbiome 

Notes

Acknowledgments

We thank Prof. Adam Godzik for assistance with editing and for his valuable comments that greatly improved the manuscript.

References

  1. Abbasian F, Lockington R, Palanisami T, Ramadass K, Megharaj M, Naidu R (2016) Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis. Biotechnol Prog 32:638–648PubMedCrossRefGoogle Scholar
  2. Abia ALK, Alisoltani A, Keshri J, Ubomba-Jaswa E (2018) Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use. Sci Total Environ 616:326–334PubMedCrossRefGoogle Scholar
  3. Abia ALK, Alisoltani A, Ubomba-Jaswa E, Dippenaar MA (2019) Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments. Sci Total Environ 655:831–841PubMedCrossRefGoogle Scholar
  4. Antwis RE, Lea JM, Unwin B, Shultz S (2018) Gut microbiome composition is associated with spatial structuring and social interactions in semi-feral Welsh Mountain ponies. Microbiome 6:207PubMedPubMedCentralCrossRefGoogle Scholar
  5. Basak P et al (2015) Spatiotemporal analysis of bacterial diversity in sediments of Sundarbans using parallel 16S rRNA gene tag sequencing. Microb Ecol 69:500–511PubMedCrossRefGoogle Scholar
  6. Bautista-de los Santos QM, Schroeder JL, Sevillano-Rivera MC, Sungthong R, Ijaz UZ, Sloan WT, Pinto AJ (2016) Emerging investigators series: microbial communities in full-scale drinking water distribution systems–a meta-analysis. Environ Sci Water Res Technol 2:631CrossRefGoogle Scholar
  7. Bell TH, Yergeau E, Juck DF, Whyte LG, Greer CW (2013a) Alteration of microbial community structure affects diesel biodegradation in an Arctic soil. FEMS Microbiol Ecol 85:51–61PubMedCrossRefGoogle Scholar
  8. Bell TH, Yergeau E, Maynard C, Juck D, Whyte LG, Greer CW (2013b) Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance. ISME J 7:1200–1210PubMedPubMedCentralCrossRefGoogle Scholar
  9. Bendia AG, Signori CN, Franco DC, Duarte RT, Bohannan BJ, Pellizari VH (2018) A mosaic of geothermal and marine features shapes microbial community structure on deception Island Volcano, Antarctica. Front Microbiol 9:899PubMedPubMedCentralCrossRefGoogle Scholar
  10. Besaury L, Ghiglione J-F, Quillet L (2014) Abundance, activity, and diversity of archaeal and bacterial communities in both uncontaminated and highly copper-contaminated marine sediments. Mar Biotechnol 16:230–242PubMedCrossRefGoogle Scholar
  11. Bolourian A, Mojtahedi Z (2018a) Immunosuppressants produced by Streptomyces: evolution, hygiene hypothesis, tumour rapalog resistance and probiotics. Environ Microbiol Rep 10:123–126PubMedCrossRefGoogle Scholar
  12. Bolourian A, Mojtahedi Z (2018b) Streptomyces, shared microbiome member of soil and gut, as ‘old friends’ against colon cancer. FEMS Microbiol Ecol 94:fiy120CrossRefGoogle Scholar
  13. Bomar L, Brugger SD, Yost BH, Davies SS, Lemon KP (2016) Corynebacterium accolens releases antipneumococcal free fatty acids from human nostril and skin surface triacylglycerols. MBio 7:e01725–e01715PubMedPubMedCentralCrossRefGoogle Scholar
  14. Brown BL et al (2015) Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River. Stand Genomic Sci 10:65PubMedPubMedCentralCrossRefGoogle Scholar
  15. Buse HY, Lu J, Lu X, Mou X, Ashbolt NJ (2014) Microbial diversities (16S and 18S rRNA gene pyrosequencing) and environmental pathogens within drinking water biofilms grown on the common premise plumbing materials unplasticized polyvinylchloride and copper. FEMS Microbiol Ecol 88:280–295PubMedCrossRefGoogle Scholar
  16. Chao Y, Mao Y, Wang Z, Zhang T (2015) Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing. Sci Rep 5:10044PubMedPubMedCentralCrossRefGoogle Scholar
  17. Chen SC, Musat N, Lechtenfeld OJ, Paschke H, Schmidt M, Said N, Popp D, Calabrese F, Stryhanyuk H, Jaekel U, Zhu YG (2019) Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature 568(7750):108PubMedCrossRefGoogle Scholar
  18. Chidamba L, Korsten L (2015) Pyrosequencing analysis of roof-harvested rainwater and river water used for domestic purposes in Luthengele village in the Eastern Cape Province of South Africa. Environ Monit Assess 187:1–17CrossRefGoogle Scholar
  19. Chung EJ, Park TS, Jeon CO, Chung YR (2012) Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 62:3030–3035PubMedCrossRefGoogle Scholar
  20. Cunha IS, Barreto CC, Costa OY, Bomfim MA, Castro AP, Kruger RH, Quirino BF (2011) Bacteria and archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe 17:118–124PubMedCrossRefGoogle Scholar
  21. de Macario EC, Macario AJ (2018) Methanogenic archaea in humans and other vertebrates: an update. In: (Endo) symbiotic methanogenic archaea. Springer, Berlin, pp 103–119Google Scholar
  22. Deng Y, Liu P, Conrad R (2019) Effect of temperature on the microbial community responsible for methane production in alkaline NamCo wetland soil. Soil Biol Biochem 132:69–79CrossRefGoogle Scholar
  23. Dombrowski N, Donaho JA, Gutierrez T, Seitz KW, Teske AP, Baker BJ (2016) Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. Nat Microbiol 1:16057PubMedCrossRefGoogle Scholar
  24. Farhat M, Moletta-Denat M, Frère J, Onillon S, Trouilhé MC, Robine E (2012) Effects of disinfection on Legionella spp., eukarya, and biofilms in a hot water system. Appl Environ Microbiol 78(19):6850–6858PubMedPubMedCentralCrossRefGoogle Scholar
  25. Flandroy L et al (2018) The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Sci Total Environ 627:1018–1038PubMedCrossRefGoogle Scholar
  26. Foulger R et al (2015) Representing virus-host interactions and other multi-organism processes in the gene ontology. BMC Microbiol 15:146PubMedPubMedCentralCrossRefGoogle Scholar
  27. Francis CA, Beman JM, Kuypers MM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1:19PubMedCrossRefGoogle Scholar
  28. Gosalbes MJ et al (2011) Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 6:e17447PubMedPubMedCentralCrossRefGoogle Scholar
  29. Grice EA et al (2009) Topographical and temporal diversity of the human skin microbiome. Science 324:1190–1192PubMedPubMedCentralCrossRefGoogle Scholar
  30. Haggerty JM, Dinsdale EA (2017) Distinct biogeographical patterns of marine bacterial taxonomy and functional genes. Glob Ecol Biogeogr 26:177–190CrossRefGoogle Scholar
  31. Henderson G et al (2015) Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 5:14567PubMedPubMedCentralCrossRefGoogle Scholar
  32. Hsu TK, Wu SF, Hsu BM, Kao PM, Tao CW, Shen SM, Ji WT, Huang WC, Fan CW (2015) Surveillance of parasitic Legionella in surface waters by using immunomagnetic separation and amoebae enrichment. Pathog Glob Health 109(7):328–335PubMedPubMedCentralCrossRefGoogle Scholar
  33. Hu Y et al (2013) Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun 4:2151PubMedCrossRefGoogle Scholar
  34. Huse SM, Ye Y, Zhou Y, Fodor AA (2012) A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One 7:e34242PubMedPubMedCentralCrossRefGoogle Scholar
  35. Huttenhower C et al (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207CrossRefGoogle Scholar
  36. Huynh HT, Pignoly M, Nkamga VD, Drancourt M, Aboudharam G (2015) The repertoire of archaea cultivated from severe periodontitis. PLoS One 10:e0121565PubMedPubMedCentralCrossRefGoogle Scholar
  37. Jahan M, Zhanel GG, Sparling R, Holley RA (2015) Horizontal transfer of antibiotic resistance from Enterococcus faecium of fermented meat origin to clinical isolates of E. faecium and Enterococcus faecalis. Int J Food Microbiol 199:78–85PubMedCrossRefGoogle Scholar
  38. Jeon EM, Kim HJ, Jung K, Kim JH, Kim MY, Kim YP, Ka J-O (2011) Impact of Asian dust events on airborne bacterial community assessed by molecular analyses. Atmos Environ 45:4313–4321CrossRefGoogle Scholar
  39. Johnson SS, Chevrette MG, Ehlmann BL, Benison KC (2015) Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment. PLoS One 10:e0122869PubMedPubMedCentralCrossRefGoogle Scholar
  40. Jordaan K, Bezuidenhout C (2016) Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality. Environ Sci Pollut Res 23:5868–5880CrossRefGoogle Scholar
  41. Kamika I, Azizi S, Tekere M (2016) Microbial profiling of South African acid mine water samples using next-generation sequencing platform. Appl Microbiol Biotechnol:1–11Google Scholar
  42. Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C (2015) High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput Biol 11:e1004557PubMedPubMedCentralCrossRefGoogle Scholar
  43. Keshri J, Mankazana BB, Momba MN (2015) Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform. Appl Microbiol Biotechnol 99:3233–3242PubMedCrossRefGoogle Scholar
  44. Kirs M et al (2017) Rainwater harvesting in American Samoa: current practices and indicative health risks. Environ Sci Pollut Res 24:12384–12392CrossRefGoogle Scholar
  45. Kostka JE et al (2011) Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Appl Environ Microbiol 77:7962–7974PubMedPubMedCentralCrossRefGoogle Scholar
  46. Långmark J, Storey MV, Ashbolt NJ, Stenström T-A (2005) Accumulation and fate of microorganisms and microspheres in biofilms formed in a pilot-scale water distribution system. Appl Environ Microbiol 71:706–712PubMedPubMedCentralCrossRefGoogle Scholar
  47. Lechevallier MW, Cawthon CD, Lee RG (1988) Factors promoting survival of bacteria in chlorinated water supplies. Appl Environ Microbiol 54:649–654PubMedPubMedCentralGoogle Scholar
  48. Lee SA et al (2016) Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and-independent approaches. J Microbiol 54:823–831PubMedCrossRefGoogle Scholar
  49. Leewis M-C et al (2016) Differential impacts of willow and mineral fertilizer on bacterial communities and biodegradation in diesel fuel oil-contaminated soil. Front Microbiol 7Google Scholar
  50. Lennard K et al (2018) Microbial composition predicts genital tract inflammation and persistent bacterial vaginosis in South African adolescent females. Infect Immun 86:e00410–e00417PubMedGoogle Scholar
  51. Li X, Rui J, Mao Y, Yannarell A, Mackie R (2014) Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar. Soil Biol Biochem 68:392–401CrossRefGoogle Scholar
  52. Lin W, Yu Z, Chen X, Liu R, Zhang H (2013) Molecular characterization of natural biofilms from household taps with different materials: PVC, stainless steel, and cast iron in drinking water distribution system. Appl Microbiol Biotechnol 97(18):8393–8401PubMedCrossRefGoogle Scholar
  53. Louca S, Parfrey LW, Doebeli M (2016) Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272–1277PubMedCrossRefGoogle Scholar
  54. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R (2012) Diversity, stability and resilience of the human gut microbiota. Nature 489:220PubMedPubMedCentralCrossRefGoogle Scholar
  55. Ma X, Baron JL, Vikram A, Stout JE, Bibby K (2015) Fungal diversity and presence of potentially pathogenic fungi in a hospital hot water system treated with on-site monochloramine. Water Res 71:197–206PubMedCrossRefGoogle Scholar
  56. Meidute S, Demoling F, Bååth E (2008) Antagonistic and synergistic effects of fungal and bacterial growth in soil after adding different carbon and nitrogen sources. Soil Biol Biochem 40:2334–2343CrossRefGoogle Scholar
  57. Mirete S, Morgante V, González-Pastor JE (2016) Functional metagenomics of extreme environments. Curr Opin Biotechnol 38:143–149CrossRefGoogle Scholar
  58. Mitchell CM et al (2015) Colonization of the upper genital tract by vaginal bacterial species in nonpregnant women. Am J Obstet Gynecol 212:611. e611–611. e619CrossRefGoogle Scholar
  59. Moissl-Eichinger C, Probst AJ, Birarda G, Auerbach A, Koskinen K, Wolf P, Holman H-YN (2017) Human age and skin physiology shape diversity and abundance of archaea on skin. Sci Rep 7:4039PubMedPubMedCentralCrossRefGoogle Scholar
  60. Müller O, Wilson B, Paulsen ML, Rumińska A, Armo HR, Bratbak G, Øvreås L (2018) Spatiotemporal dynamics of ammonia-oxidizing thaumarchaeota in distinct arctic water masses. Front Microbiol 9:24PubMedPubMedCentralCrossRefGoogle Scholar
  61. Nacke H, Fischer C, Thürmer A, Meinicke P, Daniel R (2014) Land use type significantly affects microbial gene transcription in soil. Microb Ecol 67:919–930PubMedCrossRefGoogle Scholar
  62. Navarro-Noya YE, Suárez-Arriaga MC, Rojas-Valdes A, Montoya-Ciriaco NM, Gómez-Acata S, Fernández-Luqueño F, Dendooven L (2013) Pyrosequencing analysis of the bacterial community in drinking water wells. Microb Ecol 66:19–29PubMedCrossRefGoogle Scholar
  63. Nkamga VD, Henrissat B, Drancourt M (2017) Archaea: essential inhabitants of the human digestive microbiota. Hum Microbiome J 3:1–8CrossRefGoogle Scholar
  64. Oxley AP et al (2010) Halophilic archaea in the human intestinal mucosa. Environ Microbiol 12:2398–2410PubMedCrossRefGoogle Scholar
  65. Polymenakou PN (2012) Atmosphere: a source of pathogenic or beneficial microbes? Atmosphere 3:87–102CrossRefGoogle Scholar
  66. Polymenakou PN, Mandalakis M, Stephanou EG, Tselepides A (2007) Particle size distribution of airborne microorganisms and pathogens during an intense African dust event in the eastern Mediterranean. Environ Health Perspect 116:292–296PubMedCentralCrossRefPubMedGoogle Scholar
  67. Prest E, El-Chakhtoura J, Hammes F, Saikaly P, Van Loosdrecht M, Vrouwenvelder JS (2014) Combining flow cytometry and 16S rRNA gene pyrosequencing: a promising approach for drinking water monitoring and characterization. Water Res 63:179–189PubMedCrossRefGoogle Scholar
  68. Quatrini R, Johnson DB (2018) Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH. Curr Opin Microbiol 43:139–147CrossRefGoogle Scholar
  69. Ramadass K, Megharaj M, Venkateswarlu K, Naidu R (2016) Soil bacterial strains with heavy metal resistance and high potential in degrading diesel oil and n-alkanes. Int J Environ Sci Technol 13:2863–2874CrossRefGoogle Scholar
  70. Raman R, Tharakaraman K, Sasisekharan V, Sasisekharan R (2016) Glycan–protein interactions in viral pathogenesis. Curr Opin Struct Biol 40:153–162PubMedPubMedCentralCrossRefGoogle Scholar
  71. Ramsey MM, Freire MO, Gabrilska RA, Rumbaugh KP, Lemon KP (2016) Staphylococcus aureus shifts toward commensalism in response to Corynebacterium species. Front Microbiol 7:1230PubMedPubMedCentralCrossRefGoogle Scholar
  72. Raymann K, Moeller AH, Goodman AL, Ochman H (2017) Unexplored archaeal diversity in the great ape gut microbiome. MSphere 2:e00026–e00017PubMedPubMedCentralCrossRefGoogle Scholar
  73. Reese AT, Lulow K, David LA, Wright JP (2018) Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms. Ecol Evol 8:1196–1205PubMedCrossRefGoogle Scholar
  74. Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA (2019) Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column. ISME J:1Google Scholar
  75. Revetta R, Gomez‐Alvarez V, Gerke T, Santo Domingo J, Ashbolt N (2016) Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system. J Appl MicrobiolGoogle Scholar
  76. Reza MS et al (2018) Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream, the Tama River, Tokyo. Fish Sci 84:563–577CrossRefGoogle Scholar
  77. Richards CL, Broadaway SC, Eggers MJ, Doyle J, Pyle BH, Camper AK, Ford TE (2015) Detection of pathogenic and non-pathogenic bacteria in drinking water and associated biofilms on the crow reservation, Montana, USA. Microb Ecol:1–12Google Scholar
  78. Rojas TCG, Lobo FP, Hongo JA, Vicentini R, Verma R, Maluta RP, da Silveira WD (2017) Genome-wide survey of genes under positive selection in avian pathogenic Escherichia coli strains. Foodborne Pathog Dis 14:245–252PubMedCrossRefPubMedCentralGoogle Scholar
  79. Saleem F, Mustafa A, Kori JA, Hussain MS, Kamran Azim M (2018) Metagenomic characterization of bacterial communities in drinking water supply system of a mega city. Microb Ecol 76:899–910PubMedCrossRefPubMedCentralGoogle Scholar
  80. Samad A, Trognitz F, Compant S, Antonielli L, Sessitsch A (2017) Shared and host‐specific microbiome diversity and functioning of grapevine and accompanying weed plants. Environ Microbiol 19:1407–1424PubMedCrossRefPubMedCentralGoogle Scholar
  81. Sekar S, Zintchem AA, Keshri J, Kamika I, Momba MN (2014) Bacterial profiling in brine samples of the Emalahleni water reclamation plant, South Africa, using 454-pyrosequencing method. FEMS Microbiol Lett 359:55–63PubMedCrossRefGoogle Scholar
  82. Selden R, Widdowson P, Brooker P (2016) A reader’s guide to contemporary literary theory. Routledge, LondonGoogle Scholar
  83. Serrano-Silva N, Calderon-Ezquerro MC (2018) Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods. Environ Pollut 235:20–29PubMedCrossRefGoogle Scholar
  84. Seyler LM, McGuinness LM, Kerkhof LJ (2014) Crenarchaeal heterotrophy in salt marsh sediments. ISME J 8:1534PubMedPubMedCentralCrossRefGoogle Scholar
  85. Shahi A, Aydin S, Ince B, Ince O (2016) Reconstruction of bacterial community structure and variation for enhanced petroleum hydrocarbons degradation through biostimulation of oil contaminated soil. Chem Eng J 306:60–66CrossRefGoogle Scholar
  86. Singh P, Jain K, Desai C, Tiwari O, Madamwar D (2019) Microbial community dynamics of extremophiles/extreme environment. In: Microbial diversity in the genomic era. Elsevier, p 323–332Google Scholar
  87. Smets W, Moretti S, Denys S, Lebeer S (2016) Airborne bacteria in the atmosphere: presence, purpose, and potential. Atmos Environ 139:214–221CrossRefGoogle Scholar
  88. Steele JA et al (2011) Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J 5:1414PubMedPubMedCentralCrossRefGoogle Scholar
  89. Suriya J, Shekar MC, Nathani NM, Suganya T, Bharathiraja S, Krishnan M (2017) Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River. Appl Microbiol Biotechnol 101(2):831–841PubMedCrossRefGoogle Scholar
  90. Sutton NB et al (2013) Impact of long-term diesel contamination on soil microbial community structure. Appl Environ Microbiol 79:619–630PubMedPubMedCentralCrossRefGoogle Scholar
  91. Tully BJ (2019) Metabolic diversity within the globally abundant marine group II Euryarchaea offers insight into ecological patterns. Nat Commun 10:271PubMedPubMedCentralCrossRefGoogle Scholar
  92. Turnbaugh PJ et al (2009) A core gut microbiome in obese and lean twins. Nature 457:480PubMedCrossRefGoogle Scholar
  93. Violle C, Nemergut DR, Pu Z, Jiang L (2011) Phylogenetic limiting similarity and competitive exclusion. Ecol Lett 14:782–787PubMedCrossRefGoogle Scholar
  94. Wang L, Xu Q, Kong F, Yang Y, Wu D, Mishra S, Li Y (2016) Exploring the goat rumen microbiome from seven days to two years. PLoS One 11:e0154354PubMedPubMedCentralCrossRefGoogle Scholar
  95. Wingender J, Flemming H-C (2011) Biofilms in drinking water and their role as reservoir for pathogens. Int J Hyg Environ Health 214:417–423PubMedCrossRefGoogle Scholar
  96. Wirth R et al (2018) The planktonic core microbiome and core functions in the cattle rumen by next generation sequencing. Front Microbiol 9:2285PubMedPubMedCentralCrossRefGoogle Scholar
  97. Xi C, Zhang Y, Marrs CF, Ye W, Simon C, Foxman B, Nriagu J (2009) Prevalence of antibiotic resistance in drinking water treatment and distribution systems. Appl Environ Microbiol 75:5714–5718PubMedPubMedCentralCrossRefGoogle Scholar
  98. Yang Y, Wang N, Guo X, Zhang Y, Ye B (2017) Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing. PLoS One 12:e0178425PubMedPubMedCentralCrossRefGoogle Scholar
  99. Yu J, Kim D, Lee T (2010) Microbial diversity in biofilms on water distribution pipes of different materials. Water Sci Technol 61:163–171PubMedCrossRefGoogle Scholar
  100. Zaura E, Keijser BJ, Huse SM, Crielaard W (2009) Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol 9:259PubMedPubMedCentralCrossRefGoogle Scholar
  101. Zhang G-Y, Zhang L-M, He J-Z, Liu F (2017) Comparison of archaeal populations in soil and their encapsulated Iron-manganese nodules in four locations spanning from north to South China. Geomicrobiol J 34:811–822CrossRefGoogle Scholar
  102. Zhou R, Zeng S, Hou D, Liu J, Weng S, He J, Huang Z (2019) Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: a case study from an aquatic environment. J Environ SciGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Arghavan Alisoltani
    • 1
    Email author
  • Akebe Luther King Abia
    • 2
  • Linda Bester
    • 2
    • 3
  1. 1.Division of Biomedical Sciences, School of MedicineUniversity of California, RiversideRiversideUSA
  2. 2.Antimicrobial Research Unit, School of Health Sciences, College of Health SciencesUniversity of KwaZulu-NatalDurbanSouth Africa
  3. 3.Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health SciencesUniversity of KwaZulu-NatalDurbanSouth Africa

Personalised recommendations