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High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite.

Mwaikono KS, Maina S, Sebastian A, Schilling M, Kapur V, Gwakisa P - BMC Microbiol. (2016)

Bottom Line: Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %.None of OTUs was found across all samples.This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.

View Article: PubMed Central - PubMed

Affiliation: Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam, Tanzania. kilazasmsn24@gmail.com.

ABSTRACT

Background: Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform.

Results: A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall 76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %), Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and Clostridium sensu stricto with FecD and Flavobacteria, Lysobacter and Commamonas to Riv. Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %. None of OTUs was found across all samples.

Conclusions: This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.

No MeSH data available.


Related in: MedlinePlus

Relative abundance of predominant bacterial phyla on dumpsite. a show the overall predominant taxa in different solid wastes pooled together. Different colours represent types of taxa and their relative abundance. b show levels of abundance of each predominant taxon when each solid waste was analysed separately. Solid biomedical waste (Biom, n =15 domestic solid waste (Dom, n = 33), faecal material of pigs on scavenging on dumpsite (FecD, n = 20) and in river sludge (Riv, n =8). Only phyla in abundance ≥ 0.1 % are shown. Bacterial taxa were assigned at 97 % sequence similarity cut-off level
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Fig1: Relative abundance of predominant bacterial phyla on dumpsite. a show the overall predominant taxa in different solid wastes pooled together. Different colours represent types of taxa and their relative abundance. b show levels of abundance of each predominant taxon when each solid waste was analysed separately. Solid biomedical waste (Biom, n =15 domestic solid waste (Dom, n = 33), faecal material of pigs on scavenging on dumpsite (FecD, n = 20) and in river sludge (Riv, n =8). Only phyla in abundance ≥ 0.1 % are shown. Bacterial taxa were assigned at 97 % sequence similarity cut-off level

Mentions: Thirty-five bacterial phyla were detected, however, only seven of these accounted for more than 93 % of all sequences. The predominant phyla were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %), Actinobacteria (3 %), Acidobacteria (2 %), Chloroflexi (2 %) and Spirochaetes (1 %). A large number of phyla were rare and had < 1 % of all sequences (Fig. 1). The unclassified bacteria at phylum level accounted for 2.4 % of all sequences. The heatmap (Additional file 3) shows the abundance and distribution of the predominant bacteria phyla on the dumpsite. When each type of solid waste was separately analysed, Proteobacteria was the most predominant in Biom (37.4 %), Dom (35.7 %) and Riv (42.5 %) solid wastes, while Firmicutes predominated in FecD (59.1 %) only. Majority of the bacterial phyla in all solid waste were rare and contributed < 0.1 % of all sequences. Biom and FecD had only 11 phyla accounted for 98.2 % and 99.7 % of all sequences, respectively. Likewise in Dom and Riv, 12 phyla accounted for 99.6 % and 99.4 % of all sequences, respectively.Fig. 1


High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite.

Mwaikono KS, Maina S, Sebastian A, Schilling M, Kapur V, Gwakisa P - BMC Microbiol. (2016)

Relative abundance of predominant bacterial phyla on dumpsite. a show the overall predominant taxa in different solid wastes pooled together. Different colours represent types of taxa and their relative abundance. b show levels of abundance of each predominant taxon when each solid waste was analysed separately. Solid biomedical waste (Biom, n =15 domestic solid waste (Dom, n = 33), faecal material of pigs on scavenging on dumpsite (FecD, n = 20) and in river sludge (Riv, n =8). Only phyla in abundance ≥ 0.1 % are shown. Bacterial taxa were assigned at 97 % sequence similarity cut-off level
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940873&req=5

Fig1: Relative abundance of predominant bacterial phyla on dumpsite. a show the overall predominant taxa in different solid wastes pooled together. Different colours represent types of taxa and their relative abundance. b show levels of abundance of each predominant taxon when each solid waste was analysed separately. Solid biomedical waste (Biom, n =15 domestic solid waste (Dom, n = 33), faecal material of pigs on scavenging on dumpsite (FecD, n = 20) and in river sludge (Riv, n =8). Only phyla in abundance ≥ 0.1 % are shown. Bacterial taxa were assigned at 97 % sequence similarity cut-off level
Mentions: Thirty-five bacterial phyla were detected, however, only seven of these accounted for more than 93 % of all sequences. The predominant phyla were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %), Actinobacteria (3 %), Acidobacteria (2 %), Chloroflexi (2 %) and Spirochaetes (1 %). A large number of phyla were rare and had < 1 % of all sequences (Fig. 1). The unclassified bacteria at phylum level accounted for 2.4 % of all sequences. The heatmap (Additional file 3) shows the abundance and distribution of the predominant bacteria phyla on the dumpsite. When each type of solid waste was separately analysed, Proteobacteria was the most predominant in Biom (37.4 %), Dom (35.7 %) and Riv (42.5 %) solid wastes, while Firmicutes predominated in FecD (59.1 %) only. Majority of the bacterial phyla in all solid waste were rare and contributed < 0.1 % of all sequences. Biom and FecD had only 11 phyla accounted for 98.2 % and 99.7 % of all sequences, respectively. Likewise in Dom and Riv, 12 phyla accounted for 99.6 % and 99.4 % of all sequences, respectively.Fig. 1

Bottom Line: Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %.None of OTUs was found across all samples.This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.

View Article: PubMed Central - PubMed

Affiliation: Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam, Tanzania. kilazasmsn24@gmail.com.

ABSTRACT

Background: Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform.

Results: A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall 76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %), Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and Clostridium sensu stricto with FecD and Flavobacteria, Lysobacter and Commamonas to Riv. Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %. None of OTUs was found across all samples.

Conclusions: This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.

No MeSH data available.


Related in: MedlinePlus