Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates

Metagenomic DNA extracted from polluted as well as control soil sample and electrophoresed on 0.8 % agarosa gel. Lane M is of marker, Lane 1, is for polluted sample (representing pooled metagenomic DNA for P1 + P2 + P3 = P) and Lane 2 is for control soil sample (representing pooled metagenomic DNA for C1 + C2 + C3 = C). Figure S2. Distribution of taxa among bacteria at rank phylum classified according to 16S rDNA using RDP classifier for both polluted as well as control sample. Figure S3. Distribution of taxa among bacteria at rank phylum classified according to lowest common ancestor (LCA) for both polluted as well as control sample. Figure S4. Comparative distribution of taxa among bacteria at rank class classified according to WebCARMA and M5NR datasets for both polluted as well as control sample. Table S1. Enzymes mapped for lipid metabolism pathways in KEEG database. (DOC 300 kb

Flexible taxonomic assignment of ambiguous sequencing reads

<p>Abstract</p> <p>Background</p> <p>To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (<it>ambiguous reads</it>) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it.</p> <p>Results</p> <p>We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter <it>q</it>. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed.</p> <p>Conclusions</p> <p>The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the <it>q </it>parameter. Validation of our results in an artificial dataset confirm that a combination of values of <it>q </it>produces the most accurate results.</p

Placental, oral and vaginal microbiomes and birth outcomes in rural Malawi

Being born too early or being born too small is the largest cause of neonatal mortality in the world. Compared to the rest of the world, Malawi has one of the largest burdens of preterm birth and neonatal stunting, with infection recognised as an important risk factor. Previous studies have used culture and molecular methods to identify bacteria that could be responsible for triggering labour and foetal growth restriction. The composition of the oral and vaginal microbiome has also been linked as the possible source of these bacteria. However, studies up to this point have been small and have not utilised the full potential of current sequencing technologies. In this thesis, I demonstrated using high-throughput sequencing of the 16S rRNA gene that certain organisms are associated with adverse birth outcomes. Contaminating bacterial taxa, PCR and sequencing error can be filtered post-sequencing to allow reliable reconstruction of microbial communities from low biomass samples such as the placenta. This revealed a specific community structure in the placenta and foetal membranes associated with severe chorioamnionitis. Analysis of communities in both matched vaginal and placental samples increased prevalence of Peptostreptococcus anaerobius, Sneathia sanguinegens and Prevotella amnii were associated with a smaller newborn size. These results provide further evidence of the important role the vaginal microbiome may play in seeding organisms found on placental tissues and therapeutic interventions could be designed to impact these communities with the goal of reducing the risk of preterm birth or intrauterine growth restriction