title: Sampling bacterial biodiversity from a highly contaminated stream flowing through a densely populated urban area in Karachi.
abstract: BACKGROUND
  Few studies have attempted to understand the complexity of microbial populations in Pakistan where infectious diseases are prevalent. This study was undertaken to assess bacterial biodiversity in Nehr-e-Khayyam a heavily polluted stream connected to the Arabian Gulf, which runs through a densely populated urban area in Karachi, Pakistan.
  
  
  METHODS
  Employing a universal pair of oligonucleotides capable of amplifying species-specific segments of 16S rRNA gene from all Eubacteria, we generated a library of PCR products using total DNA purified from the collected sample, cloned the amplifers into pGEM-T-Easy and sequenced each recombinant clone. The obtained DNA sequences were subjected to bio-informatic analyses.
  
  
  RESULTS
  A total of 71 recombinant clones were obtained from the amplified 16S rDNA products and sequenced. Bioinformatics analyses revealed that 54 (out of 71) were unique sequences from which 42 shared > 97% and 12 shared < 97% homology to their database counterparts. One sequence originated from the plastid DNA of eukaryote Pyramimonas disomata. From the remaining 53 sequences, 45 were Proteo-bacteria and 8 Fermicute in origin. Among 71 sequences, Alpha-, Beta- and Gamma-proteobacteria species constituted -86% of Proteo-bacteria identified in the sample while only -13% were Fermicutes.
  
  
  CONCLUSIONS
  The microbial niche in Nehr-e-Khayyam is occupied predominantly by heterotrophic Proteo-bacterial and Firmicute strains, some of which are known human pathogens.
authors.forename: Syed Faaiz
authors.initials: SF
authors.lastname: Enam
authors.forename: Humaira
authors.initials: H
authors.lastname: Qureshi
authors.forename: Sohail A
authors.initials: SA
authors.lastname: Qureshi
mesh_terms: D001419:Bacteria / Q000145:classification*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000032:analysis; D010154:Pakistan; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D045483:Rivers; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S