American Journal of Microbiological Research
ISSN (Print): 2328-4129 ISSN (Online): 2328-4137 Website: Editor-in-chief: Apply for this position
Open Access
Journal Browser
American Journal of Microbiological Research. 2015, 3(4), 135-143
DOI: 10.12691/ajmr-3-4-3
Open AccessArticle

16S rRNA Amplicons Survey Revealed Unprecedented Bacterial Community in Solid Biomedical Wastes

Kilaza Samson MWAIKONO1, , Solomon Maina2, Aswathy Sebastian3, Vivek Kapur1, 4 and Paul Gwakisa1, 5

1The Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania

2BecA-ILRI Hub International Livestock Research Institute, P. O. Box 30709, Nairobi, Kenya

3Departments of Biochemistry and Molecular Biology, W238A Millennium Science Complex University Park, PA 16802, Penn State University, USA

4Huck Institutes of Life Sciences, Department of Veterinary and Biomedical Sciences, 205 Wartik Laboratories, The Pennsylvania State University, University Park, PA 16802, USA

5Genome Sciences Centre, Faculty of Veterinary Medicine, Sokoine University of Agriculture, Morogoro, Tanzania

Pub. Date: August 02, 2015

Cite this paper:
Kilaza Samson MWAIKONO, Solomon Maina, Aswathy Sebastian, Vivek Kapur and Paul Gwakisa. 16S rRNA Amplicons Survey Revealed Unprecedented Bacterial Community in Solid Biomedical Wastes. American Journal of Microbiological Research. 2015; 3(4):135-143. doi: 10.12691/ajmr-3-4-3


Despite known risks of inappropriate disposal of biomedical solid waste; most cities in developing countries are still disposing unsorted and untreated solid biomedical waste in common dumpsites. While many studies reported the presence of pathogens in fresh biomedical waste from hospitals, none has reported on the abundance and diversity of bacterial community in aged solid biomedical waste from a common dumpsite. A qualitative survey was done to identify types of solid biomedical waste on the dumpsite. Soils, sludge or washings of biomedical wastes were sampled. Total DNA was extracted and v4 region of 16S rRNA amplicons were sequenced using an Illumina MiSeq platform. A total of 1,706,442 sequences from 15 samples passed quality control. The number of sequences per sample ranged from 70664 to 174456 (mean 121765, SD 35853). Diversity was high with an InvSimpson index of 63 (Range 5 – 496, SD 121). Thirty five phyla were identified, but only 9 accounted for 96% of all sequences. The dominant phyla were Proteobacteria 37.4%, Firmicutes 34.4%, Bacteroidetes 14.1 %, Actinobacteria 5.6% and Chloroflex 1.7%. Catchall analysis predicted a mean of 9399 species per sample. Overall, 31402 operational taxonomic units (OTUs) were detected, however, only 19.8% (6,202) OTUs were found more than ten times. The most predominant OTUs were Proteinclasticum (10.4%), Acinetobacter (6.9), Halomonas (3.9), Pseudomonas (1.7%), Escherichia/Shigella 1.5% and Planococcus (1.3%). Proteiniclasticum spp and Acinetobacter spp were found in 67% (10/15) of all samples at relative abundance of 1%. Taxonomic-to-phenotype mapping revealed the presence of 36.2% related to bacteria involved in dehalogenation, 11.6% degraders of aromatic hydrocarbons, 14.8% chitin degraders, 8.5% chlorophenol degradation and Atrazine metabolism 8.3%. Taxonomy-to human pathogen mapping found 34% related to human pathogens and 39.4% were unknown. Conclusions There’s rich and diverse bacterial community in aged solid biomedical waste. Some of the predominant OTUs are related to bacteria of industrial use. We found a good number of OTUs mapping to human pathogens. Most of OTUs mapped to unknown metabolism and also to group unknown whether they human pathogens or not. To our knowledge, this is the first reports on bacteria related to industrial use from solid biomedical waste. This finding will facilitate to design further research using functional metagenomics to better understand the potential of bacteria from aged solid biomedical waste.

solid biomedical waste bacteria molecular diversity 16S rRNA dumpsite illumina MiSeq Tanzania

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit


[1]  Acharya A, Gokhale VA, Joshi D: Impact of Biomedical Waste on City Environment: Case Study of Pune, India. Applied Chemistry (IOSR-JAC) 2014, 6(6):7.
[2]  Gidarakos E, Petrantonaki M, Anastasiadou K, Schramm K-W: Characterization and hazard evaluation of bottom ash produced from incinerated hospital waste. Journal of hazardous materials 2009, 172(2):935-942.
[3]  Hossain MS, Santhanam A, Norulaini NN, Omar AM: Clinical solid waste management practices and its impact on human health and environment–A review. Waste Management 2011, 31(4):754-766.
[4]  DeRoos R: Environmental concerns in hospital waste disposal. Hospitals 1974, 48(4):88 passim.
[5]  Hassan MM, Ahmed S, Rahman KA, Biswas T: Pattern of medical waste management: existing scenario in Dhaka City, Bangladesh. BMC Public Health 2008, 8(1):36.
[6]  Rastogi V, Rastogi P, Bhatia S: Bacteriological Profile of Biomedical Waste: Management Guidelines. Journal of Indian Academy of Forensic Medicine 2011, 33(2):145-148.
[7]  Boss U, Moli G, Roy G, Prasad K: Biomedical waste generation in Puducherry Government General Hospital and its management implications. Journal of environmental health 2009, 71(9):54-58.
[8]  Yadavannavar M, Berad AS, Jagirdar P: Biomedical waste management: A study of knowledge, attitude, and practices in a tertiary health care institution in Bijapur. Indian journal of community medicine: official publication of Indian Association of Preventive & Social Medicine 2010, 35(1):170.
[9]  Wallace L, Zaltzman R, Burchinal I: Where solid waste comes from; where it goes. Modem hospitals 1972, 121(3):92-95.
[10]  Saini S, Das BK, Kapil A, Nagarajan SS, Sarma R: The study of bacterial flora of different types in hospital waste: evaluation of waste treatment at AIIMS Hospital, New Delhi. Southeast Asian Journal of Tropical Medicine & Public Health 2004, 35(4):986.
[11]  Anitha J, JAYRAAJ IA: Isolation and identification of bacteria in biomedical wastes (BMW). International journal of pharmacy and pharmaceutical sciences 2012, 4(5):386-388.
[12]  Vandecandelaere I, Matthijs N, Van Nieuwerburgh F, Deforce D, Vosters P, De Bus L, Nelis HJ, Depuydt P, Coenye T: Assessment of Microbial Diversity in Biofilms Recovered from Endotracheal Tubes Using Culture Dependent and Independent Approaches. PloS one 2012, 7(6):e38401.
[13]  Riesenfeld CS, Goodman RM, Handelsman J: Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environmental Microbiology 2004, 6(9):981-989.
[14]  Oyeleke S, Istifanus N: The microbiological effects of hospital wastes on the environment. African Journal of Biotechnology 2009, 8(7).
[15]  Illumina: 16S Metagenomic Sequencing Library preparation Guide: 2013.
[16]  Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R: Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences 2011, 108(Supplement 1):4516-4522.
[17]  Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology 2009, 75(23):7537-7541.
[18]  Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids research 2013, 41(D1):D590-D596.
[19]  Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R: UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27(16):2194-2200.
[20]  Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM: Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic acids research 2014, 42(D1):D633-D642.
[21]  Chao A: Nonparametric estimation of the number of classes in a community. Scand J Stat 1984, 11:265–270.
[22]  Chao A, Lee S-M: Estimating the number of classes via sample coverage. Journal of the American statistical Association 1992, 87(417):210-217.
[23]  Chao A, Shen T-J: Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample. Environmental and ecological statistics 2003, 10(4):429-443.
[24]  Hunter PR, Gaston MA: Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. Journal of clinical microbiology 1988, 26(11):2465-2466.
[25]  Bunge J: Estimating the number of species with CatchAll. In: Pacific Symposium on Biocomputing: 2011: World Scientific; 2011: 121-130.
[26]  McMurdie PJ, Holmes S: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS one 2013, 8(4):e61217.
[27]  Meadow JF, Altrichter AE, Kembel SW, Moriyama M, O’Connor TK, Womack AM, Brown G, Green JL, Bohannan BJ: Bacterial communities on classroom surfaces vary with human contact. Microbiome 2014, 2(1):7.
[28]  Mitra S, Stärk M, Huson DH: Analysis of 16S rRNA environmental sequences using MEGAN. BMC genomics 2011, 12(Suppl 3):S17.
[29]  Hossain MS, Rahman NNNA, Balakrishnan V, Puvanesuaran VR, Sarker MZI, Kadir MOA: Infectious Risk Assessment of Unsafe Handling Practices and Management of Clinical Solid Waste. International journal of environmental research and public health 2013, 10(2):556-567.
[30]  Costa MC, Arroyo LG, Allen-Vercoe E, Stämpfli HR, Kim PT, Sturgeon A, Weese JS: Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene. PloS one 2012, 7(7):e41484.
[31]  Suchodolski JS, Markel ME, Garcia-Mazcorro JF, Unterer S, Heilmann RM, Dowd SE, Kachroo P, Ivanov I, Minamoto Y, Dillman EM: The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease. PloS one 2012, 7(12):e51907.
[32]  Suchodolski JS, Xenoulis PG, Paddock CG, Steiner JM, Jergens AE: Molecular analysis of the bacterial microbiota in duodenal biopsies from dogs with idiopathic inflammatory bowel disease. Veterinary Microbiology 2010, 142(3):394-400.
[33]  Bouchotroch S, Quesada E, Izquierdo I, Rodríguez M, Béjar V: Bacterial exopolysaccharides produced by newly discovered bacteria belonging to the genus Halomonas, isolated from hypersaline habitats in Morocco. Journal of Industrial Microbiology and Biotechnology 2000, 24(6):374-378.
[34]  Schwibbert K, Marin‐Sanguino A, Bagyan I, Heidrich G, Lentzen G, Seitz H, Rampp M, Schuster SC, Klenk HP, Pfeiffer F: A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T. Environmental Microbiology 2011, 13(8):1973-1994.
[35]  Omer MI, Gumaa SA, Hassan AA, Idris KH, Ali OA, Osman MM, Saleh MS, Mohamed NA, Khaled MM: Prevalence and Resistance Profile of Acinetobacter baumannii Clinical Isolates from a Private Hospital in Khartoum, Sudan. American Journal of Microbiological Research 2015, 3(2):76-79.
[36]  Bhattacharya A, Gupta A: Evaluation of Acinetobacter sp. B9 for Cr (VI) resistance and detoxification with potential application in bioremediation of heavy-metals-rich industrial wastewater. Environmental Science and Pollution Research 2013, 20(9):6628-6637.
[37]  Franzetti A, Gandolfi I, Fracchia L, Van Hamme J, Gkorezis P, Marchant R, Banat IM: Biosurfactant use in heavy metal removal from industrial effluents and contaminated sites. Biosurfactants: Production and Utilization—Processes, Technologies, and Economics 2014, 159:361.
[38]  Hossain MS, Santhanam A, Nik Norulaini NA, Omar AKM: Clinical solid waste management practices and its impact on human health and environment – A review. Waste Management 2011, 31(4):754-766.
[39]  Oviasogie FE, Ajuzie CU, Ighodaro UG: Bacterial Analysis of Soil From Waste Dumpsite. Archives of Applied Science Research 2010, 2(5):161-167.
[40]  Pfeifer Y, Cullik A, Witte W: Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens. International Journal of Medical Microbiology 2010, 300(6):371-379.
[41]  Ndugulile F, Jureen R, Harthug S, Urassa W, Langeland N: Extended Spectrum β-Lactamases among Gram-negative bacteria of nosocomial origin from an Intensive Care Unit of a tertiary health facility in Tanzania. BMC infectious Diseases 2005, 5(1):86.
[42]  Jensen LB, Baloda S, Boye M, Aarestrup FM: Antimicrobial resistance among Pseudomonas spp. and the Bacillus cereus group isolated from Danish agricultural soil. Environment international 2001, 26(7):581-587.
[43]  Odjadjare EE, Igbinosa EO, Mordi R, Igere B, Igeleke CL, Okoh AI: Prevalence of Multiple Antibiotics Resistant (MAR) Pseudomonas Species in the Final Effluents of Three Municipal Wastewater Treatment Facilities in South Africa. International journal of environmental research and public health 2012, 9(6):2092-2107.
[44]  Khannous L, Jrad M, Dammak M, Miladi R, Chaaben N, Khemakhem B, Gharsallah N, Fendri I: Isolation of a novel amylase and lipase-producing Pseudomonas luteola strain: study of amylase production conditions. Lipids in health and disease 2014, 13(1):9.
[45]  Miyazaki R, Bertelli C, Benaglio P, Canton J, De Coi N, Gharib WH, Gjoksi B, Goesmann A, Greub G, Harshman K et al: Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology 2015, 17(1):91-104.
[46]  Wasi S, Tabrez S, Ahmad M: Use of Pseudomonas spp. for the bioremediation of environmental pollutants: a review. Environmental monitoring and assessment 2013, 185(10):8147-8155.
[47]  Nandi RG, Joshi M, Shriwastva K: Biodegradation of polyethylene by microorganism isolated from garbage soil. Indian J Applied & Pure Bio Vol 2013, 28(2):279-281.
[48]  48.Xu G, Zheng W, Li Y, Wang S, Zhang J, Yan Y: Biodegradation of chlorpyrifos and 3, 5, 6-trichloro-2-pyridinol by a newly isolated Paracoccus sp. strain TRP. International biodeterioration & biodegradation 2008, 62(1):51-56.
[49]  Dziewit L, Dmowski M, Baj J, Bartosik D: The plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries genes for the degradation of N, N-dimethylformamide (DMF), whose expression is activated by a LuxR-family regulator. Applied and environmental microbiology 2010.
[50]  Huang C-J, Lin H, Yang X: Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements. Journal of industrial microbiology & biotechnology 2012, 39(3):383-399.
[51]  Thakker C, Martínez I, San KY, Bennett GN: Succinate production in Escherichia coli. Biotechnology journal 2012, 7(2):213-224.
[52]  Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY: Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nature biotechnology 2013, 31(2):170-174.
[53]  Zhang K, Song L, Dong X: Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen. International journal of systematic and evolutionary microbiology 2010, 60(9): 2221-2225.
[54]  Desta AF, Assefa F, Leta S, Stomeo F, Wamalwa M, Njahira M, Appolinaire D: Microbial Community Structure and Diversity in an Integrated System of Anaerobic-Aerobic Reactors and a Constructed Wetland for the Treatment of Tannery Wastewater in Modjo, Ethiopia. PloS one 2014, 9(12): e115576.
[55]  Khan NH, Bondici VF, Medihala PG, Lawrence JR, Wolfaardt GM, Warner J, Korber DR: Bacterial diversity and composition of an alkaline uranium mine tailings-water interface. Journal of Microbiology 2013, 51(5): 558-569.
[56]  Vester JK, Glaring MA, Stougaard P: Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing. Microb Cell Fact 2014, 13:72.
[57]  Subramanian S: Bioprospecting of moderately halophilic bacteria planococcus sp vitp21 for cr vi reduction under high salt condition. 2015.
[58]  Vennila R, Kannan V: Bioremediation of petroleum refinery effluent by Planococcus halophilus. African Journal of Biotechnology 2013, 10(44): 8829-8833.
[59]  Essghaier B, Rouaissi M, Boudabous A, Jijakli H, Sadfi-Zouaoui N: Production and partial characterization of chitinase from a halotolerant Planococcus rifitoensis strain M2-26. World Journal of Microbiology and Biotechnology 2010, 26(6): 977-984.