eng Science and Education Publishing Journal of Applied & Environmental Microbiology 2373-6712 2018-08-21 6 2 42 50 10.12691/jaem-6-2-3 JAEM2018623 article Kilaza Samson Mwaikono kilazasmsn24@gmail.com 1 2 Solomon Maina 3 Paul Gwakisa 3 4 Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, P.O. Box 2958, Dar es Salaam, Tanzania BecA-ILRI Hub International Livestock Research Institute, P. O. Box 30709, Nairobi, Kenya Free-range food animals scavenging in urban and peri-urban dumpsites are exposed to diverse microbes of public health importance, yet little is known of their fecal microbiota and public health implication. We characterized the fecal microbiota of pigs scavenging at a municipal dumpsite (FecD, n =19) by MiSeq sequencing for 16S rRNA and compared with conventionally indoor reared pigs (FecI, n = 21). A total of 4,364,507 sequences with an average of 114,852 reads per sample passed quality control. The predicted mean of species per sample was 5,979. There was no difference in alpha diversity between free-range and indoor pigs (InvSimpson 23.68 vs 38.06, p = 0.1091 and Shannon 5.60 vs 6.41, p = 0.053). The community membership and population structure were significantly different (Yue and Clayton p = 0.001 and Jaccard p = 0.014). Bacterial genera significantly associated with free-range pigs were Bifidobacterium, Enterococcus, Turicibacter and Cellulosilyticus; while in indoor pigs were Prevotella, Fibrobacter, Megasphaera, Allisonella, fibrobacteres and Phascolarctobacterium. Metagenome prediction revealed that Tetracycline biosynthesis, Staphylococcus infection, sporulation and Vibrio cholerae pathogenic pathways are significantly (p < 0.05) associated with scavenging pigs. The organism-level phenotype prediction revealed that free-range pigs were also dominated with Proteobacteria rich in mobile elements and pathogenic potential. Free-range pigs scavenging in urban and peri-urban areas are potential reservoirs of pathogens of public health importance. These findings suggest indoor management of animals in urban and peri-urban areas to mitigate possible health risks from free-range animals which might get into food chain. Further study of the gut microflora of free-range pigs at dumpsites and their clinical significance to humans and other animals is warranted. http://pubs.sciepub.com/jaem/6/2/3/jaem-6-2-3.pdf pigs fecal microbiota 16S rRNA municipal dumpsites free-range pigs scavenging