Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu Y-X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG (2019) Nat Biotechnol 37(9):1091–1091 ‘Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2’. https://doi.org/10.1038/s41587-019-0252-6

Bor B, Bedree JK, Shi W, McLean JS, He X (2019) Saccharibacteria (TM7) in the human oral Microbiome. J Dent Res 98(5):500–509. https://doi.org/10.1177/0022034519831671

Article  CAS  PubMed  PubMed Central  Google Scholar 

Caucci S, Karkman A, Cacace D, Rybicki M, Timpel P, Voolaid V, Gurke R, Virta M, Berendonk TU (2016) Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow. FEMS Microbiol Ecol 92(5):fiw060. https://doi.org/10.1093/femsec/fiw060

Article  CAS  PubMed  Google Scholar 

Chahal C, van den Akker B, Young F, Franco C, Blackbeard J, Monis P (2016) Chapter Two - Pathogen and Particle associations in Wastewater: significance and implications for treatment and disinfection processes. In: Sariaslani S, Michael Gadd G (eds) Advances in Applied Microbiology. Academic. https://doi.org/10.1016/bs.aambs.2016.08.001.

Chang S-C, Kao M-R, Saldivar RK, Díaz-Moreno SM, Xing X, Furlanetto V, Yayo J, Divne C, Vilaplana F, Abbott DW, Hsieh YSY (2023) The Gram-positive bacterium Romboutsia Ilealis harbors a polysaccharide synthase that can produce (1,3;1,4)-β-D-glucans. Nat Commun 14(1):4526. https://doi.org/10.1038/s41467-023-40214-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng J, Zhou L, Wang H (2024) Symbiotic microbial communities in various locations of the lung cancer respiratory tract along with potential host immunological processes affected. Front Cell Infect Microbiol 14. https://www.frontiersin.org/articles/https://doi.org/10.3389/fcimb.2024.1296295accessed 4 March 2024

Cong W, Stuart B, AIhusein N, Liu B, Tang Y, Wang H, Wang Y, Manchundiya A, Lambert H (2022) Antibiotic use and bacterial infection in COVID-19 patients in the second phase of the SARS-CoV-2 pandemic: a scoping review. Antibiotics 11(8):991. https://doi.org/10.3390/antibiotics11080991

Article  CAS  PubMed  PubMed Central  Google Scholar 

Davies J, Davies D (2010) Origins and Evolution of Antibiotic Resistance. Microbiol Mol Biology Reviews: MMBR 74(3):417–433. https://doi.org/10.1128/MMBR.00016-10

Article  CAS  PubMed Central  Google Scholar 

Harnisz M, Kiedrzyńska E, Kiedrzyński M, Korzeniewska E, Czatzkowska M, Koniuszewska I, Jóźwik A, Szklarek S, Niestępski S, Zalewski M (2020) The impact of WWTP size and sampling season on the prevalence of antibiotic resistance genes in wastewater and the river system. Sci Total Environ 741:140466. https://doi.org/10.1016/j.scitotenv.2020.140466

Article  CAS  PubMed  Google Scholar 

Hu Z, Yang L, Liu Z, Han J, Zhao Y, Jin Y, Sheng Y, Zhu L, Hu B (2023) Excessive disinfection aggravated the environmental prevalence of antimicrobial resistance during COVID-19 pandemic. Sci Total Environ 882:163598. https://doi.org/10.1016/j.scitotenv.2023.163598

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl Environ Microbiol 67(1):411–419. https://doi.org/10.1128/AEM.67.1.411-419.2001

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hung Y-M, Lu T-P, Tsai M-H, Lai L-C, Chuang EY (2021) EasyMAP: a user-friendly online platform for analyzing 16S ribosomal DNA sequencing data. New Biotechnol 63:37–44. https://doi.org/10.1016/j.nbt.2021.03.001

Article  CAS  Google Scholar 

Johansson MHK, Aarestrup FM, Petersen TN (2023) Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world. PLoS ONE 18(10):e0293169. https://doi.org/10.1371/journal.pone.0293169

Article  CAS  PubMed  PubMed Central  Google Scholar 

Johar AA, Salih MA, Abdelrahman HA, Mana HA, Hadi HA, Eltai NO (2023) Wastewater-based epidemiology for tracking bacterial diversity and antibiotic resistance in COVID-19 isolation hospitals in Qatar. J Hosp Infect 141:209–220. https://doi.org/10.1016/j.jhin.2023.08.011

Article  CAS  PubMed  Google Scholar 

Kietsiri P, Muangnapoh C, Lurchachaiwong W, Lertsethtakarn P, Bodhidatta L, Suthienkul O, Waters NC, Demons ST, Vesely BA (2021) Characterization of Arcobacter Spp. Isolated from human diarrheal, non-diarrheal and food samples in Thailand. PLoS ONE 16(2):e0246598. https://doi.org/10.1371/journal.pone.0246598

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31(9):814–821. https://doi.org/10.1038/nbt.2676

Article  CAS  PubMed  PubMed Central  Google Scholar 

Malik SS, Mundra S (2022) Increasing consumption of antibiotics during the COVID-19 pandemic: implications for Patient Health and Emerging Anti-microbial Resistance. Antibiotics 12(1):45. https://doi.org/10.3390/antibiotics12010045

Article  CAS  PubMed  PubMed Central  Google Scholar 

Neu AT, Allen EE, Roy K (2021) ‘Defining and quantifying the core microbiome: Challenges and prospects’, Proceedings of the National Academy of Sciences, 118(51):e2104429118, https://doi.org/10.1073/pnas.2104429118

Numberger D, Ganzert L, Zoccarato L, Mühldorfer K, Sauer S, Grossart H-P, Greenwood AD (2019) Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing. Sci Rep 9(1):9673. https://doi.org/10.1038/s41598-019-46015-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Patterson EI, Prince T, Anderson ER, Casas-Sanchez A, Smith SL, Cansado-Utrilla C, Solomon T, Griffiths MJ, Acosta-Serrano Á, Turtle L, Hughes GL (2020) Methods of inactivation of SARS-CoV-2 for downstream biological assays. J Infect Dis 222(9):1462–1467. https://doi.org/10.1093/infdis/jiaa507

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rezasoltani S, Yadegar A, Hatami B, Asadzadeh Aghdaei H, Zali MR (2020) Antimicrobial Resistance as a hidden menace lurking behind the COVID-19 outbreak: The Global impacts of too much Hygiene on AMR. Front Microbiol 11. https://www.frontiersin.org/articles/https://doi.org/10.3389/fmicb.2020.590683accessed 9 February 2023

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12(6):R60. https://doi.org/10.1186/gb-2011-12-6-r60

Article  PubMed  PubMed Central  Google Scholar 

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. https://doi.org/10.1128/AEM.03448-12

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shannon KE, Lee D-Y, Trevors JT, Beaudette LA (2007) Application of real-time quantitative PCR for the detection of selected bacterial pathogens during municipal wastewater treatment. Sci Total Environ 382(1):121–129. https://doi.org/10.1016/j.scitotenv.2007.02.039

Article  CAS  PubMed  Google Scholar 

Song Y, Jia J, Liu D, Choi L, Wang G, Li M (2017) Sediminibacterium roseum sp. nov., isolated from sewage sediment. Int J Syst Evol MicroBiol 67(11):4674–4679. https://doi.org/10.1099/ijsem.0.002355

Article  CAS  PubMed  Google Scholar 

van den Berg MF, Botes M, Slabbert E, Cloete TE (2016) Evaluating sulphate removal and identifying the bacterial community present in acid mine drainage treated with synthetic domestic wastewater sludge. Water SA 42(3):475–482. https://doi.org/10.4314/wsa.v42i3.13

Article  CAS  Google Scholar 

Volmer JG, McRae H, Morrison M (2023) The evolving role of methanogenic archaea in mammalian microbiomes. Front Microbiol 14:1268451. https://doi.org/10.3389/fmicb.2023.1268451

Article  PubMed  PubMed Central  Google Scholar 

Wang C, Mantilla-Calderon D, Xiong Y, Alkahtani M, Bashawri YM, Al Qarni H, Hong P-Y (2022) Investigation of antibiotic Resistome in Hospital Wastewater during the COVID-19 pandemic: is the initial phase of the pandemic contributing to Antimicrobial Resistance? Environ Sci Technol 56(21):15007–15018. https://doi.org/10.1021/acs.est.2c01834

Article  CAS  PubMed  PubMed Central  Google Sch