Abstract
Human sewage pollution is a major threat to public health because sewage always comes with pathogens. Human sewage is usually received and treated by wastewater treatment plants (WWTPs) to control pathogenic risks and ameliorate environmental health. However, untreated sewage that flows into water environments may cause serious waterborne diseases, as reported in India and Bangladesh. To examine the fate of the human sewage microbiome in a local municipal WWTP of Hong Kong, we used massively parallel sequencing of 16S rRNA gene to systematically profile microbial communities in samples from three sections (i.e., influent, activated sludge, and effluent) obtained monthly throughout 1 year. The results indicated that: (1) influent sewage bacterial profile reflected the human microbiome; (2) human gut bacterial community was the dominant force shaping influent sewage bacterial profile; (3) most human sewage bacteria could be effectively removed by the WWTP; (4) a total of 75 genera were profiled as potentially pathogenic bacteria, most of which were still present in the effluent although at a very low level; (5) a grouped pattern of bacterial community was observed among the same section samples but a dispersed pattern was found among the different section samples; and (6) activated sludge was less affected by the influent sewage bacteria, but it showed a significant impact on the effluent bacteria. All of these findings provide novel insights toward a mechanistic understanding of the fate of human sewage microbiome in the WWTP.
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Ahmed W, Richardson K, Sidhu JPS, Toze S (2012) Escherichia coli and Enterococcus spp. in rainwater tank samples: comparison of culture-based methods and 23S rRNA gene quantitative PCR assays. Environ Sci Technol 46(20):11370–11376
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin JJ, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Weissenbach J, Ehrlich SD, Bork P, Consortium M (2011) Enterotypes of the human gut microbiome. Nature 473(7346):174–180
Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Meth 55(3):541–555
Baumann B, Snozzi M, Zehnder AJ, Van Der Meer JR (1996) Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic–anaerobic changes. J Bacteriol 178(15):4367–4374
Cai L, Ye L, Tong AH, Lok S, Zhang T (2013) Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets. PLoS One 8(1):e53649
Cai L, Zhang T (2013) Detecting human bacterial pathogens in wastewater treatment plants by a high-throughput shotgun sequencing technique. Environ Sci Technol 47(10):5433–5441
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336
Chen GX, Walker SL (2012) Fecal indicator bacteria transport and deposition in saturated and unsaturated porous media. Environ Sci Technol 46(16):8782–8790
Claesson MJ, Wang QO, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38(22):e200
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37(Database issue):D141–D145
Dubinsky EA, Esmaili L, Hulls JR, Cao YP, Griffith JF, Andersen GL (2012) Application of phylogenetic microarray analysis to discriminate sources of fecal pollution. Environ Sci Technol 46(8):4340–4347
Facklam R (2002) What happened to the Streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15(4):613–630
Ferguson AS, Layton AC, Mailloux BJ, Culligan PJ, Williams DE, Smartt AE, Sayler GS, Feighery J, McKay LD, Knappett PS, Alexandrova E, Arbit T, Emch M, Escamilla V, Ahmed KM, Alam MJ, Streatfield PK, Yunus M, van Geen A (2012) Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater. Sci Total Environ 431:314–322
Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, Kostka S, Prinz H (2000) Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17. J Bacteriol 182(17):4677–4687
Funke G, Frodl R, Sommer H (2004) First comprehensively documented case of Paracoccus yeei infection in a human. J Clin Microbiol 42(7):3366–3368
Gordon KV, Brownell M, Wang SY, Lepo JE, Mott J, Nathaniel R, Kilgen M, Hellein KN, Kennedy E, Harwood VJ (2013) Relationship of human-associated microbial source tracking markers with Enterococci in Gulf of Mexico waters. Water Res 47(3):996–1004
Guo F, Zhang T (2013) Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing. Appl Microbiol Biotechnol 97(10):4607–4616
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH et al (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214
Jeanneau L, Solecki O, Wery N, Jarde E, Gourmelon M, Communal PY, Jadas-Hecart A, Caprais MP, Gruau G, Pourcher AM (2012) Relative decay of fecal indicator bacteria and human-associated markers: a microcosm study simulating wastewater input into seawater and freshwater. Environ Sci Technol 46(4):2375–2382
Kohler W (2007) The present state of species within the genera Streptococcus and Enterococcus. Int J Med Microbiol 297(3):133–150
LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M (2013) Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotech 24(2):160–168
Lee JE, Lee S, Sung J, Ko G (2011) Analysis of human and animal fecal microbiota for microbial source tracking. ISME J 5(2):362–365
Liu ZP, Wang BJ, Liu XY, Dai X, Liu YH, Liu SJ (2008) Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969. Int J Syst Evol Microbiol 58(Pt 1):257–261
Machado-Ferreira E, Piesman J, Zeidner NS, Soares CA (2012) A prevalent alpha-proteobacterium Paracoccus sp. in a population of the Cayenne ticks (Amblyomma cajennense) from Rio de Janeiro, Brazil. Genet Mol Biol 35(4):862–867
McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML (2010) Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12(2):378–392
McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML (2013) Sewage reflects the distribution of human faecal Lachnospiraceae. Environ Microbiol 15(8):2213–2227
Murugan K, Prabhakaran P, Al-Sohaibani S, Sekar K (2012) Identification of source of faecal pollution of Tirumanimuttar River, Tamilnadu, India using microbial source tracking. Environ Monit Assess 184(10):6001–6012
Newton RJ, VandeWalle JL, Borchardt MA, Gorelick MH, McLellan SL (2011) Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor. Appl Environ Microbiol 77(19):6972–6981
Pandey PK, Verma P, Kumar H, Bavdekar A, Patole MS, Shouche YS (2012) Comparative analysis of fecal microflora of healthy full-term Indian infants born with different methods of delivery (vaginal vs cesarean): Acinetobacter sp. prevalence in vaginally born infants. J Biosci 37(6):989–998
Pickering AJ, Julian TR, Marks SJ, Mattioli MC, Boehm AB, Schwab KJ, Davis J (2012) Fecal contamination and diarrheal pathogens on surfaces and in soils among Tanzanian households with and without improved sanitation. Environ Sci Technol 46(11):5736–5743
Prakash S, Tomaro-Duchesneau C, Saha S, Cantor A (2011) The gut microbiota and human health with an emphasis on the use of microencapsulated bacterial cells. J Biomed Biotechnol 2011:981214
Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ (2011) Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A 108(Suppl 1):4680–4687
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P (2013) Genomic variation landscape of the human gut microbiome. Nature 493(7430):45–50
Shanks OC, Newton RJ, Kelty CA, Huse SM, Sogin ML, McLellan SL (2013) Comparison of the microbial community structures of untreated wastewaters from different geographic locales. Appl Environ Microbiol 79(9):2906–2913
Shanks OC, Sivaganesan M, Peed L, Kelty CA, Blackwood AD, Greene MR, Noble RT, Bushon RN, Stelzer EA, Kinzelman J, Anan'eva T, Sinigalliano C, Wanless D, Griffith J, Cao YP, Weisberg S, Harwood VJ, Staley C, Oshima KH, Varma M, Haugland RA (2012) Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria. Environ Sci Technol 46(2):945–953
Sidhu JP, Hodgers L, Ahmed W, Chong MN, Toze S (2012) Prevalence of human pathogens and indicators in stormwater runoff in Brisbane, Australia. Water Res 46(20):6652–6660
Staley C, Reckhow KH, Lukasik J, Harwood VJ (2012) Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake. Water Res 46(17):5799–5812
Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG (2010) Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol 44(20):7777–7782
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261–5267
Wery N, Monteil C, Pourcher AM, Godon JJ (2010) Human-specific fecal bacteria in wastewater treatment plant effluents. Water Res 44(6):1873–1883
Woolhouse M, Gowtage-Sequeria S, Evans B (2006) T16: quantitative analysis of the characteristics of emerging and re-emerging human pathogens. Centre for Infectious Diseases, University of Edinburgh
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227
Zhang T, Shao MF, Ye L (2012) 454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J 6(6):1137–1147
Zheng Q, Wang Y, Chen C, Xia X, Fu Y, Zhang R, Jiao N (2011) Paracoccus beibuensis sp. nov., isolated from the South China Sea. Curr Microbiol 62(3):710–714
Acknowledgments
Dr. Lin Cai thanks The University of Hong Kong for the Postdoctoral Fellowship. The authors wish to thank Agnes Chan and Wilson Chan for their technical support and service on 454 pyrosequencing. The authors also acknowledge the Research Grants Council of Hong Kong for the financial support of this study (HKU7201/11E).
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Cai, L., Ju, F. & Zhang, T. Tracking human sewage microbiome in a municipal wastewater treatment plant. Appl Microbiol Biotechnol 98, 3317–3326 (2014). https://doi.org/10.1007/s00253-013-5402-z
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DOI: https://doi.org/10.1007/s00253-013-5402-z