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

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, Lysobacterand 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

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support

Validation of chromatographic method for the determination of melatonin in wine and grapes using high performance liquid chromatography-fluorescence detection

This master research project reports two validated methods for determination of melatonin in wine using high performance liquid chromatography and fluorescence detector

Molecular Diversity of Bacteria from a Municipal Dumpsite: Implications to Public Health

Despite known risks of inappropriate disposal of solid wastes; most cities in developing countries dispose waste in open dumpsite where humans, animals and microbes interact. This study was done in Arusha municipal dumpsite, Tanzania to investigate the abundance and diversity of bacteria, compare the faecal microbiota of pigs scavenging on dumpsite and indoor reared pigs, and also determine the resistance profile of enteric bacteria from the dumpsite. Domestic wastes, solid biomedical wastes, sludge from the river near the dumpsite and faecal materials of pigs were sampled. Total DNA was extracted and the variable region four (v4) of the 16S rRNA gene was sequenced using high throughput Illumina MiSeq platform. The quality control of sequences and the statistical analyses was performed using Mothur platform. A total of 8,469,294 quality sequences were generated. The mean of bacterial species per sample was 8,243. Diversity was high with an average InvSimpson index of 44.2. Thirty-five bacterial phyla dominated by Firmicutes (38%), Proteobacteria (35%), Bacteroidetes (13%) and Actinobacteria (3%) were found. Overall, 76,862 operational taxonomic units (OTUs) dominated by Acinetobacter (12.1%), Clostridium sensu stricto (4.8%), Proteinclasticum and Lactobacillus (each 3.4%), Enterococcus (2.9%) and Escherichia/Shigella (1.7%) were revealed. There was a significant difference in faecal microbiota between scavenging and indoor reared pigs. Pathogenic genera like Brucella, Rickettsia and Listeria were exclusive to scavenging pigs. In solid biomedical waste, 36.2% of OTUs were related to dehalogenation, 11.6% degraders of aromatic hydrocarbons, 8.5% chlorophenol degradation and Atrazine metabolism 8.3%, and bacteria related to pathogens were 34%. Escherichia/ Shigella, Bacilli and Proteiniclasticum were predominant enteric bacteria. Some bacteria in scavenging pigs had 99% sequence similarity to pathogenic Escherichia furgosonii, Shigella sonnei, Enterococcus faecium and Escherichia coli O154:H4. Over 50% of the isolates were multidrug resistant. The study provides a comprehensive report on diversity of bacteria in Arusha municipal dumpsite. The high species richness 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 dumpsites

Prevalence and Antimicrobial Resistance Phenotype of Enteric Bacteria from a Municipal Dumpsite

Research Article published by Science and Education Publishing Vol. 3, No. 3, 2015,The objective of the study was to determine the prevalence and antibiotic resistance phenotype of enteric bacteria from the municipal dumpsite. A qualitative survey of the dumpsite was conducted to identify types of solid wastes and nature of interaction on the dumpsite. Samples were collected from different type of solid waste, including domestic waste (Dom), solid biomedical waste (Biom), river sludge near the dumpsite (Riv) and faecal material of pigs scavenging on the dumpsite (FecD). A control sample was collected from faecal material of pigs initially reared indoor (FecI) and shifted to scavenging on the dumpsite (FecIF). Total genomic DNA was extracted, and the 16S rRNA gene was amplified, sequenced and used to study prevalence of enteric bacteria. The same sample was used to isolate enteric bacteria that were later tested to 8 different antibiotics for their susceptibility phenotype. Solid wastes are not sorted in Arusha municipal. There was high interaction between animals and humans on the dumpsite. A total of 219 enteric bacteria from 75 genera were identified. Escherichia sp and Shigella sp (12%), Bacillus sp (11%) and Proteiniclasticum (4%) were the predominant genera. Most of the Escherichia sp, Shigella sp and Bacillus were from FecD, while Proteiniclasticum spp was from Biom. Some isolates from FecD had 99% sequence similarity to pathogenic Escherichia furgosonii, Shigella sonnei, Enterococcus faecium and Escherichia coli O154:H4. Over 50% of the isolates were resistant to Penicillin G, Ceftazidime and Nalidixic Acid. Ciprofloxacin and Gentamycin were the most effective antibiotics with 81% and 79% susceptible isolates, respectively. Of all the isolates, 56% (45/80) were multidrug resistant. Escherichia sp and Bacillus sp (12 isolates each) constituted a large group of multidrug resistant bacteria. All Pseudomonas sp from Biom and FecD were multidrug resistant. There is high prevalence of antibiotic resistant enteric bacteria on the dumpsite. We report possible risks of spreading antibiotic resistant bacteria/genes from the dumpsite to clinical settings through animals and humans interacting on the dumpsite. This finding calls for a comprehensive research to study the shared resistome in bacteria from the environment, humans and animals using PCR and metagenomic based approaches to identify prevalence of known and capture new resistant genes

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

Research Article published by Science and Education Publishing Vol. 3, No. 4, 2015Despite 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

Inauguration of the Tanzania Society of Human Genetics:Biomedical Research in Tanzania with Emphasis on Human Genetics and Genomics

Human genetics research and applications are rapidly growing areas in health innovations and services. African populations are reported to be highly diverse and carry the greatest number of variants per genome. Exploring these variants is key to realize the genomic medicine initiative. However, African populations are grossly underrepresented in various genomic databases, which has alerted scientists to address this issue with urgency. In Tanzania, human genetics research and services are conducted in different institutions on both communicable and noncommunicable diseases. However, there is poor coordination of the research activities, often leading to limited application of the research findings and poor utilization of available resources. In addition, contributions from Tanzanian human genetics research and services are not fully communicated to the government, national, and international communities. To address this scientific gap, the Tanzania Society of Human Genetics (TSHG) has been formed to bring together all stakeholders of human genetics activities in Tanzania and to formally bring Tanzania as a member to the African Society of Human Genetics. This article describes the inauguration event of the TSHG, which took place in November 2019. It provides a justification for its establishment and discusses presentations from invited speakers who took part in the inauguration of the TSHG