Skip to main content
Log in

Advanced microbial analysis for wastewater quality monitoring: metagenomics trend

  • Mini-Review
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Urban Wastewater treatment plants (UWWTPs) have played an important and fundamental role in society for water purification of contaminated human wastewaters over the last decades. Microorganisms are very important in UWWTP as their metabolic activity significantly reduces the organic load of the UWW, although there is an uncertain gap in our knowledge regarding microbial consortium structure and their activity in UWWTP operation on a large scale. On the other hand, effluents of UWWTPs have come to be a new source of fresh water to ease water scarcity in many regions of the world, especially in intensive irrigation practices. Many concerns over health risks relating to the direct reuse of this water are very well known. However, if a proper disinfection treatment is applied, these are strongly reduced as conventional methodologies have demonstrated over the last decades. In line with this, the continuous development of new devices for analytical measurement that increase the sensitivities (limit of detection) are showing that other potential risks for both environmental and human health may be associated with UWW reuse. In this work, the most important aspects related to microorganisms in UWWTPs and UWW effluents are presented. Moreover, the new developments on genetic tools for detection of microorganisms are presented, with special emphasis on metagenomic methodology. A bibliometric analysis of what has been published so far is also carried out.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Allegra S, Berger F, Berthelot P, Grattard F, Pozzetto B, Riffard S (2008) Use of flow cytometry to monitor Legionella viability. Appl Environ Microbiol 74:7813–7816. https://doi.org/10.1128/AEM.01364-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM (2009) A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS One. https://doi.org/10.1371/journal.pone.0006372

  • American Public Health Association (APHA) (2005) Standard methods for the examination of water & wastewater. In: Eaton AD, Clesceri LS, Rice EW, Greenberg AE, Franson MAH (eds), 21st edn. APHA, Washington

  • Amos GCA, Zhang L, Hawkey PM, Gaze WH, Wellington EM (2014) Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes. Vet Microbiol 171:441–447. https://doi.org/10.1016/j.vetmic.2014.02.017

    Article  CAS  PubMed  Google Scholar 

  • Aracic S, Manna S, Petrovski S, Wiltshire JL, Mann G, Franks AE (2015) Innovative biological approaches for monitoring and improving water quality. Front Microbiol. https://doi.org/10.3389/fmicb.2015.00826

  • Asano T (1998) Wastewater reclamation and reuse, water quality management library, vol 10. Technomic Publishing Company, Lancaster

  • Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach CF, Fick J, Kristiansson E, Tysklind M, Larsson DGJ (2016) Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Sci Total Environ 572:697–712. https://doi.org/10.1016/j.scitotenv.2016.06.228

    Article  CAS  PubMed  Google Scholar 

  • Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IMJ, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DMD, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E, Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang G-D, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O’Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59. https://doi.org/10.1038/nature07517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brayner R, Couté A, Livage J, Perrette C, Sicard C (2011) Micro-algal biosensors. Anal Bioanal Chem 401:581–597

    Article  CAS  PubMed  Google Scholar 

  • Cao C, Lou I, Huang C, Lee M-Y (2016) Metagenomic sequencing of activated sludge filamentous bacteria community using the Ion Torrent platform. Desalin Water Treat 57:2175–2183. https://doi.org/10.1080/19443994.2014.979447

    Article  CAS  Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624. https://doi.org/10.1038/ismej.2012.8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108(Suppl):4516–4522. https://doi.org/10.1073/pnas.1000080107

    Article  CAS  PubMed  Google Scholar 

  • Chakraborty R, Wu CH, Hazen TC (2012) Systems biology approach to bioremediation. Curr Opin Biotechnol 23:483–490

    Article  CAS  PubMed  Google Scholar 

  • Chouler J, Di Lorenzo M (2015) Water quality monitoring in developing countries; can microbial fuel cells be the answer? Biosensors 5:450–470

    Article  PubMed  PubMed Central  Google Scholar 

  • Chowdhury A, Mannan SBIN, Mazumdar RM (2012) Pyrosequencing—principles and applications. Int J Life Sci Pharma Res 2:65–76

    Google Scholar 

  • Cydzik-Kwiatkowska A, Zielińska M (2016) Bacterial communities in full-scale wastewater treatment systems. World J Microbiol Biotechnol 32:66. https://doi.org/10.1007/s11274-016-2012-9

    Article  PubMed  PubMed Central  Google Scholar 

  • DWA (2011) Green drop report, 2010-2011. Department of Water Affairs, Pretoria

  • Eyers L, George I, Schuler L, Stenuit B, Agathos SN, El Fantroussi S (2004) Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl Microbiol Biotechnol 66:123–130

    Article  CAS  PubMed  Google Scholar 

  • Ferro G, Polo-López MI, Fernández-Ibáñez P (2016) Conventional and new processes for urban wastewater disinfection: effect on emerging and resistant microorganisms. Handb Environ Chem 45:107–128. https://doi.org/10.1007/698-2015-390

    Google Scholar 

  • Garrido-Cardenas JA, Garcia-Maroto F, Alvarez-Bermejo JA, Manzano-Agugliaro F (2017) DNA sequencing sensors : an overview. Sensors (Basel) 17(3):1–15. https://doi.org/10.3390/s17030588

    Article  Google Scholar 

  • Garrido-Cardenas JA, Manzano-Agugliaro F (2017) The metagenomics worldwide research. Curr Genet. https://doi.org/10.1007/s00294-017-0693-8

  • Giannakis S, Lόpez MIP, Spuhler D, Pérez JAS, Ibáñez PF, Pulgarin C (2016) Solar disinfection is an augmentable, in situ-generated photo-Fenton reaction—part 2: a review of the applications for drinking water and wastewater disinfection. Appl Catal B Environ 198:431–446

    Article  CAS  Google Scholar 

  • Gilbride KA, Lee DY, Beaudette LA (2006) Molecular techniques in wastewater: understanding microbial communities, detecting pathogens, and real-time process control. J Microbiol Methods 66:1–20

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez-Silva BM, Rønning AJ, Andreassen IK, Bakke I, Cervantes FJ, Østgaard K, Vadstein O (2017) Changes in the microbial community of an anammox consortium during adaptation to marine conditions revealed by 454 pyrosequencing. Appl Microbiol Biotechnol. https://doi.org/10.1007/s00253-017-8160-5

  • Gorchev HG, Ozolins G (2011) WHO guidelines for drinking-water quality. WHO Chron 38:104–108. https://doi.org/10.1016/S1462-0758(00)00006-6

    Google Scholar 

  • Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249. https://doi.org/10.1016/S1074-5521(98)90108-9

    Article  CAS  PubMed  Google Scholar 

  • Huang K, Tang J, Zhang X-X, Xu K, Ren H (2014) A comprehensive insight into tetracycline resistant bacteria and antibiotic resistance genes in activated sludge using next-generation sequencing. Int J Mol Sci 15:10083–10100. https://doi.org/10.3390/ijms150610083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hyman ED (1988) A new method of sequencing DNA. Anal Biochem 174:423–436. https://doi.org/10.1016/0003-2697(88)90041-3

    Article  CAS  PubMed  Google Scholar 

  • Jianrong C, Yuqing M, Nongyue H, Xiaohua W, Sijiao L (2004) Nanotechnology and biosensors. Biotechnol Adv 22:505–518

    Article  PubMed  Google Scholar 

  • Kau AL, Ahern PP, Griffin NW, Goodman AL, Jeffrey I (2012) Human nutrition, the gut microbiome, and immune system: envisioning the future. Nature 474:327–336. https://doi.org/10.1038/nature10213.Human

    Article  Google Scholar 

  • Kimes N, Callaghan A, Aktas D, Smith W, Sunner J, Golding B, Drozdowska M, Hazen T, Suflita J, Morris P (2013) Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the deepwater horizon oil spill. Front Microbiol 4:1–17. https://doi.org/10.3389/fmicb.2013.00050

    Article  Google Scholar 

  • Lagarde F, Jaffrezic-Renault N (2011) Cell-based electrochemical biosensors for water quality assessment. Anal Bioanal Chem 400:947–964

    Article  CAS  PubMed  Google Scholar 

  • Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Østerås M, Schrenzel J, François P (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods 79:266–271. https://doi.org/10.1016/j.mimet.2009.09.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lazarova V, Bahri A (2005) Water reuse for irrigation: agriculture, landscapes, and turf grass. CRC Press, Boca Raton

  • Lee DJ, Chang JS, Lai JY (2015) Microalgae-microbial fuel cell: a mini review. Bioresour Technol 198:891–895

    Article  CAS  PubMed  Google Scholar 

  • Lee H, Gurtowski J, Yoo S, Nattestad M, Marcus S, Goodwin S, McCombie WR, Schatz M (2016) Third-generation sequencing and the future of genomics. bioRxiv:48603. https://doi.org/10.1101/048603

  • Ley RE (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26:5–11. https://doi.org/10.1097/MOG.0b013e328333d751

    Article  PubMed  Google Scholar 

  • Li RW (2011) Metagenomics and its applications in agriculture, biomedicine, and environmental studies. Nova Science Publisher’s

  • Liebl W, Angelov A, Juergensen J, Chow J, Loeschcke A, Drepper T, Classen T, Pietruzska J, Ehrenreich A, Streit WR, Jaeger KE (2014) Alternative hosts for functional (meta)genome analysis. Appl Microbiol Biotechnol 98:8099–8109

    Article  CAS  PubMed  Google Scholar 

  • Lin W, Yu Z, Zhang H, Thompson IP (2014) Diversity and dynamics of microbial communities at each step of treatment plant for potable water generation. Water Res 52:218–230. https://doi.org/10.1016/j.watres.2013.10.071

    Article  CAS  PubMed  Google Scholar 

  • Loman NJ, Watson M (2015) Successful test launch for nanopore sequencing. Nat Methods 12:303–304. https://doi.org/10.1038/nmeth.3327

    Article  CAS  PubMed  Google Scholar 

  • Lovley DR (2003) Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 1:35–44. https://doi.org/10.1038/nrmicro731

    Article  CAS  PubMed  Google Scholar 

  • Lu X, Zhang XX, Wang Z, Huang K, Wang Y, Liang W, Tan Y, Liu B, Tang J (2015) Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing. PLoS One. https://doi.org/10.1371/journal.pone.0125549

  • Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One. https://doi.org/10.1371/journal.pone.0030087

  • Ma Q, Qu Y, Shen W, Zhang Z, Wang J, Liu Z, Li D, Li H, Zhou J (2015) Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing. Bioresour Technol 179:436–443. https://doi.org/10.1016/j.biortech.2014.12.041

    Article  CAS  PubMed  Google Scholar 

  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402. https://doi.org/10.1146/annurev.genom.9.081307.164359

    Article  CAS  PubMed  Google Scholar 

  • Merriman B, Torrent I, Rothberg JM (2012) Progress in Ion Torrent semiconductor chip based sequencing. Electrophoresis 33:3397–3417

    Article  CAS  PubMed  Google Scholar 

  • Miralles-Cuevas S, Oller I, Agüera A, Pérez JAS, Sánchez-Moreno R, Malato S, Gernjak W (2016) Is the combination of nanofiltration membranes and AOPs for removing microcontaminants cost effective in real municipal wastewater effluents? Environ Sci Water Res Technol 2:511–520. https://doi.org/10.1039/C6EW00001K

    Article  CAS  Google Scholar 

  • Morgan XC, Segata N, Huttenhower C (2013) Biodiversity and functional genomics in the human microbiome. Trends Genet 29:51–58

    Article  CAS  PubMed  Google Scholar 

  • National Water Quality Management, S (2006) Australia guidelines for water recycling. National water quality management strategy (Biotext Pt). Cambera. Retrieved from: http://www.environment.gov.au/system/files/resources/044e7a7e-558a-4abf-b985-2e831d8f36d1/files/water-recycling-guidelines-health-environmental-21.pdf

  • Oliver GR, Hart SN, Klee EW (2015) Bioinformatics for clinical next generation sequencing. Clin Chem 61:124–135

    Article  CAS  PubMed  Google Scholar 

  • Oller I, Malato S, Sánchez-Pérez JA (2011) Combination of advanced oxidation processes and biological treatments for wastewater decontamination—a review. Sci Total Environ 409:4141–4166

    Article  CAS  PubMed  Google Scholar 

  • Ordovas JM, Mooser V (2006) Metagenomics: the role of the microbiome in cardiovascular diseases. Curr Opin Lipidol 17:157–161. https://doi.org/10.1097/01.mol.0000217897.75068.ba

    Article  CAS  PubMed  Google Scholar 

  • Pace N, Stahl D, Lane D, Olsen G (1985) Analyzing natural microbial populations by rRNA sequences. ASM Am Soc Microbiol News 51:4–12

    Google Scholar 

  • Park M, Tsai SL, Chen W (2013) Microbial biosensors: engineered microorganisms as the sensing machinery. Sensors (Basel) 13:5777–5795

    Article  CAS  Google Scholar 

  • Pescod MB (1992) Wastewater treatment and use in agriculture

  • Qiu L, Chen Z-Y, Lu D-Y, Hu H, Wang Y-T (2014) Public funding and private investment for R&D: a survey in China’s pharmaceutical industry. Health Res Policy Syst 12:27. https://doi.org/10.1186/1478-4505-12-27

    Article  PubMed  PubMed Central  Google Scholar 

  • Ranasinghe PD, Satoh H, Oshiki M, Oshima K, Suda W, Hattori M, Mino T (2012) Revealing microbial community structures in large- and small-scale activated sludge systems by barcoded pyrosequencing of 16S rRNA gene. Water Sci Technol 66:2155–2161. https://doi.org/10.2166/wst.2012.428

    Article  CAS  PubMed  Google Scholar 

  • Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394. https://doi.org/10.1146/annurev.micro.57.030502.090759

    Article  PubMed  Google Scholar 

  • Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics, Proteomics Bioinforma 13:278–289

    Article  Google Scholar 

  • Rizzo L, Manaia C, Merlin C, Schwartz T, Dagot C, Ploy MC, Michael I, Fatta-Kassinos D (2013) Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. Sci Total Environ 447:345–360

    Article  CAS  PubMed  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547. https://doi.org/10.1128/AEM.66.6.2541-2547.2000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santoro DO, Cardoso AM, Coutinho FH, Pinto LH, Vieira RP, Albano RM, Clementino MM (2015) Diversity and antibiotic resistance profiles of pseudomonads from a hospital wastewater treatment plant. J Appl Microbiol 119:1527–1540. https://doi.org/10.1111/jam.12936

    Article  CAS  PubMed  Google Scholar 

  • Sanz JL, Köchling T (2007) Molecular biology techniques used in wastewater treatment: an overview. Process Biochem 42:119–133

    Article  CAS  Google Scholar 

  • Seder N, Abdel-Jabbar S (2011) Safe use of treated wastewater in agriculture Jordan case study. Prepared for ACWUA.

  • Suenaga H, Ohnuki T, Miyazaki K (2007) Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Env Microbiol 9:2289–2297. https://doi.org/10.1111/j.1462-2920.2007.01342.x

    Article  CAS  Google Scholar 

  • Tun HM, Brar MS, Khin N, Jun L, Hui RKH, Dowd SE, Leung FCC (2012) Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. J Microbiol Methods 88:369–376. https://doi.org/10.1016/j.mimet.2012.01.001

    Article  CAS  PubMed  Google Scholar 

  • Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051–1063. https://doi.org/10.1101/gr.076463.108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van der Mark EJ, Liu G, Verberk JQJC, Van Dijk JC (2013) Flow cytometry total cell counts: a field study assessing microbiological water quality and growth in unchlorinated drinking water distribution systems. Biomed Res Int 1–10

  • Van Nevel S, Koetzsch S, Proctor C, Prest E, Vrouwenvelder J, Knezev A, Boon N, Hammes F (2017) Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring. https://doi.org/10.1016/j.watres.2017.01.065

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y-H, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74. https://doi.org/10.1126/science.1093857

    Article  CAS  PubMed  Google Scholar 

  • Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS (2015) Application of metagenomics in the human gut microbiome. World J Gastroenterol 21:803–814

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang Y, Yu K, Xia Y, Lau FTK, Tang DTW, Fung WC, Fang HHP, Zhang T (2014) Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants. Appl Microbiol Biotechnol 98:5709–5718. https://doi.org/10.1007/s00253-014-5648-0

    Article  CAS  PubMed  Google Scholar 

  • Yazmín Ramírez-Castillo F, Loera-Muro A, Jacques M, Garneau P, Avelar-González FJ, Harel J, Lilián Guerrero-Barrera A (2015) Waterborne pathogens: detection methods and challenges. Pathogens 4:307–334. https://doi.org/10.3390/pathogens4020307

    Article  Google Scholar 

  • Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Bohm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P (2014) Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol 10:766–766. https://doi.org/10.15252/msb.20145645

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang T, Yang Y, Pruden A (2015) Effect of temperature on removal of antibiotic resistance genes by anaerobic digestion of activated sludge revealed by metagenomic approach. Appl Microbiol Biotechnol 99:7771–7779. https://doi.org/10.1007/s00253-015-6688-9

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This study was funded by the Spanish Ministry of Economy and Competitiveness through the collaborative TRICERATOPS project (CTQ2015-69832-C4-1-R) and WATER4FOOD project (CTQ2014-54563-C3).)

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jose Antonio Garrido-Cardenas.

Ethics declarations

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of interest

The authors declare that they have no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Garrido-Cardenas, J.A., Polo-López, M.I. & Oller-Alberola, I. Advanced microbial analysis for wastewater quality monitoring: metagenomics trend. Appl Microbiol Biotechnol 101, 7445–7458 (2017). https://doi.org/10.1007/s00253-017-8490-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-017-8490-3

Keywords

Navigation