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

Kilaza Samson MWAIKONO^1, , Solomon Maina², Aswathy Sebastian³, Vivek Kapur^{1, 4} and Paul Gwakisa^{1, 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

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

Abstract

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.

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

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